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

2019 ◽  
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 ◽  
Data Mining Approach ◽  
Double Stranded Dna ◽  
Wide Range ◽  
The Family ◽  
Linear Dsdna ◽  
Dsdna Viruses

AbstractPolintons (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 viruses that remain 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 animal-specific viruses with two genus-level divisions. We suggest 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.

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.

scholarly journals ATP serves as a nucleotide switch coupling the genome maturation and packaging motor complexes of a virus assembly machine

2020 ◽  
Vol 48 (9) ◽  
pp. 5006-5015
Author(s):  
Qin Yang ◽  
Carlos E Catalano
Keyword(s):  
Atp Hydrolysis ◽  
Virus Assembly ◽  
Genome Packaging ◽  
Dna Viruses ◽  
Motor Complex ◽  
Double Stranded Dna ◽  
Tightly Coupled ◽  
Switch Mechanism ◽  
Genome Maturation ◽  
Dsdna Viruses

Abstract The assembly of double-stranded DNA viruses, from phages to herpesviruses, is strongly conserved. Terminase enzymes processively excise and package monomeric genomes from a concatemeric DNA substrate. The enzymes cycle between a stable maturation complex that introduces site-specific nicks into the duplex and a dynamic motor complex that rapidly translocates DNA into a procapsid shell, fueled by ATP hydrolysis. These tightly coupled reactions are catalyzed by terminase assembled into two functionally distinct nucleoprotein complexes; the maturation complex and the packaging motor complex, respectively. We describe the effects of nucleotides on the assembly of a catalytically competent maturation complex on viral DNA, their effect on maturation complex stability and their requirement for the transition to active packaging motor complex. ATP plays a major role in regulating all of these activities and may serve as a ‘nucleotide switch’ that mediates transitions between the two complexes during processive genome packaging. These biological processes are recapitulated in all of the dsDNA viruses that package monomeric genomes from concatemeric DNA substrates and the nucleotide switch mechanism may have broad biological implications with respect to virus assembly mechanisms.

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 Molecular fossils reveal ancient associations of dsDNA viruses with several phyla of fungi

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Zhen Gong ◽  
Yu Zhang ◽  
Guan-Zhu Han
Keyword(s):  
Giant Virus ◽  
Virus Infections ◽  
Dsdna Virus ◽  
Dna Viruses ◽  
Molecular Fossils ◽  
Double Stranded Dna ◽  
Fungal Genomes ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Dsdna Viruses

Abstract Little is known about the infections of double-stranded DNA (dsDNA) viruses in fungi. Here, we use a paleovirological method to systematically identify the footprints of past dsDNA virus infections within the fungal genomes. We uncover two distinct groups of endogenous nucleocytoplasmic large DNA viruses (NCLDVs) in at least seven fungal phyla (accounting for about a third of known fungal phyla), revealing an unprecedented diversity of dsDNA viruses in fungi. Interestingly, one fungal dsDNA virus lineage infecting six fungal phyla is closely related to the giant virus Pithovirus, suggesting giant virus relatives might widely infect fungi. Co-speciation analyses indicate fungal NCLDVs mainly evolved through cross-species transmission. Taken together, our findings provide novel insights into the diversity and evolution of NCLDVs in fungi.

scholarly journals Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Nicholas P. Stone ◽  
Gabriel Demo ◽  
Emily Agnello ◽  
Brian A. Kelch
Keyword(s):  
Major Capsid Protein ◽  
Extreme Environment ◽  
Structural Basis ◽  
Genome Packaging ◽  
Virus Capsid ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
High Internal Pressure ◽  
Extracellular Environment ◽  
Catch Bonds

Abstract The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.

scholarly journals A virus of hyperthermophilic archaea with a unique architecture among DNA viruses

2016 ◽  
Vol 113 (9) ◽  
pp. 2478-2483 ◽  
Author(s):  
Elena Ilka Rensen ◽  
Tomohiro Mochizuki ◽  
Emmanuelle Quemin ◽  
Stefan Schouten ◽  
Mart Krupovic ◽  
...  
Keyword(s):  
Ebola Virus ◽  
Inner Core ◽  
Genetic Material ◽  
Marburg Virus ◽  
Hyperthermophilic Archaea ◽  
Virion Protein ◽  
Host Cell Membrane ◽  
Dna Viruses ◽  
The Family ◽  
Linear Dsdna

Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus,Pyrobaculumfilamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the familyFiloviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.

scholarly journals Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

2019 ◽  
Vol 116 (39) ◽  
pp. 19585-19592 ◽  
Author(s):  
Julien Guglielmini ◽  
Anthony C. Woo ◽  
Mart Krupovic ◽  
Patrick Forterre ◽  
Morgan Gaia
Keyword(s):  
Phylogenetic Trees ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Eukaryotic Dna ◽  
Dsdna Viruses ◽  
Virion Formation ◽  
Intense Debate ◽  
Core Genes

Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

scholarly journals A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Thomas W. Allain ◽  
Grant D. Stentiford ◽  
David Bass ◽  
Donald C. Behringer ◽  
Jamie Bojko
Keyword(s):  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Open Reading Frames ◽  
The Novel ◽  
Dna Viruses ◽  
Gene Synteny ◽  
Double Stranded Dna ◽  
The Family ◽  
Novel Virus ◽  
Dikerogammarus Haemobaphes

Abstract The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).

scholarly journals Temperature effects on virion volume and genome length in dsDNA viruses

2016 ◽  
Vol 12 (3) ◽  
pp. 20160023 ◽  
Author(s):  
Rachel L. Nifong ◽  
James F. Gillooly
Keyword(s):  
Environmental Temperature ◽  
Size Variation ◽  
Genome Length ◽  
Dsdna Virus ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Virus Size ◽  
Dsdna Viruses ◽  
Gene Overlap ◽  
Growth And Reproduction

Heterogeneity in rates of survival, growth and reproduction among viruses is related to virus particle (i.e. virion) size, but we have little understanding of the factors that govern the four to five orders of magnitude in virus size variation. Here, we analyse variation in virion size in 67 double-stranded DNA viruses (i.e. dsDNA) that span all major biomes, and infect organisms ranging from single-celled prokaryotes to multicellular eukaryotes. We find that two metrics of virion size (i.e. virion volume and genome length) decrease by about 55-fold as the temperature of occurrence increases from 0 to 40°C. We also find that gene overlap increases exponentially with temperature, such that smaller viruses have proportionally greater gene overlap at higher temperatures. These results indicate dsDNA virus size increases with environmental temperature in much the same way as the cell or genome size of many host species.

scholarly journals Virulent Poxviruses Inhibit DNA Sensing by Preventing STING Activation

2018 ◽  
Vol 92 (10) ◽  
Author(s):  
Iliana Georgana ◽  
Rebecca P. Sumner ◽  
Greg J. Towers ◽  
Carlos Maluquer de Motes
Keyword(s):  
Endoplasmic Reticulum ◽  
Vaccinia Virus ◽  
Immune Activation ◽  
Cellular Mechanism ◽  
Innate Immune ◽  
Dna Sensing ◽  
Dna Viruses ◽  
Pathogen Invasion ◽  
Double Stranded Dna ◽  
Wide Range

ABSTRACT Cytosolic recognition of DNA has emerged as a critical cellular mechanism of host immune activation upon pathogen invasion. The central cytosolic DNA sensor cGAS activates STING, which is phosphorylated, dimerizes and translocates from the endoplasmic reticulum (ER) to a perinuclear region to mediate IRF-3 activation. Poxviruses are double-stranded DNA viruses replicating in the cytosol and hence likely to trigger cytosolic DNA sensing. Here, we investigated the activation of innate immune signaling by 4 different strains of the prototypic poxvirus vaccinia virus (VACV) in a cell line proficient in DNA sensing. Infection with the attenuated VACV strain MVA activated IRF-3 via cGAS and STING, and accordingly STING dimerized and was phosphorylated during MVA infection. Conversely, VACV strains Copenhagen and Western Reserve inhibited STING dimerization and phosphorylation during infection and in response to transfected DNA and cyclic GMP-AMP, thus efficiently suppressing DNA sensing and IRF-3 activation. A VACV deletion mutant lacking protein C16, thought to be the only viral DNA sensing inhibitor acting upstream of STING, retained the ability to block STING activation. Similar inhibition of DNA-induced STING activation was also observed for cowpox and ectromelia viruses. Our data demonstrate that virulent poxviruses possess mechanisms for targeting DNA sensing at the level of the cGAS-STING axis and that these mechanisms do not operate in replication-defective strains such as MVA. These findings shed light on the role of cellular DNA sensing in poxvirus-host interactions and will open new avenues to determine its impact on VACV immunogenicity and virulence. IMPORTANCE Poxviruses are double-stranded DNA viruses infecting a wide range of vertebrates and include the causative agent of smallpox (variola virus) and its vaccine vaccinia virus (VACV). Despite smallpox eradication VACV remains of interest as a therapeutic. Attenuated strains are popular vaccine candidates, whereas replication-competent strains are emerging as efficient oncolytics in virotherapy. The successful therapeutic use of VACV depends on a detailed understanding of its ability to modulate host innate immune responses. DNA sensing is a critical cellular mechanism for pathogen detection and activation of innate immunity that is centrally coordinated by the endoplasmic reticulum-resident protein STING. Here, STING is shown to mediate immune activation in response to MVA, but not in response to virulent VACV strains or other virulent poxviruses, which prevent STING activation and DNA sensing during infection and after DNA transfection. These results provide new insights into poxvirus immune evasion and have implications in the rational design of VACV-based therapeutics.

Sign in / Sign up

Export Citation Format

Share Document