scholarly journals Unique viruses that infect Archaea related to eukaryotes

2021 ◽  
Author(s):  
Ian Rambo ◽  
Valerie De Anda ◽  
Marguerite Langwig ◽  
Brett Baker
Keyword(s):  
Deep Sea ◽  
Structural Proteins ◽  
Genome Replication ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Double Stranded Dna ◽  
Archaeal Viruses ◽  
Hydrothermal Sediments ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Globally Distributed

Abstract Asgard archaea are globally distributed, newly described microbes related to eukaryotes. Despite their importance, Asgard viruses have not been described. Here we characterize seven double-stranded DNA (dsDNA) viral genomes that infected Lokiarchaeota, Helarchaeota, and Thorarchaeota in deep-sea hydrothermal sediments. These viruses code for Caudovirales-like structural proteins, as well as proteins distinct from those described in archaeal viruses. They contain genes common in eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs), and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications, and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Recovery of these Asgard viral genomes reveals they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their roles in the ecology and evolution of their hosts.

scholarly journals Unique viruses that infect Archaea related to eukaryotes

2021 ◽  
Author(s):  
Ian M Rambo ◽  
Valerie De Anda ◽  
Marguerite V Langwig ◽  
Brett J Baker
Keyword(s):  
Transcriptional Regulation ◽  
Deep Sea ◽  
Structural Proteins ◽  
Genome Replication ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Archaeal Viruses ◽  
Hydrothermal Sediments ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Globally Distributed

Asgard archaea are newly described microbes that are related to eukaryotes. Asgards are diverse and globally distributed, however, their viruses have not been described. Here we characterize seven viral genomes that infected Lokiarchaeota, Helarchaeota, and Thorarchaeota in deep-sea hydrothermal sediments. These viruses code for structural proteins similar to those in Caudovirales, as well as proteins distinct from those described in archaeal viruses. They also have genes common in eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs), and are predicted to be capable of semi-autonomous genome replication, repair, epigenetic modifications, and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. This first glimpse of Asgard viruses reveals they have features of both prokaryotic and eukaryotic viruses, and provides insights into their roles in the ecology and evolution of these globally distributed microbes.

scholarly journals Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species

2020 ◽  
Vol 165 (11) ◽  
pp. 2723-2731 ◽  
Author(s):  
Tatiana A. Demina ◽  
Hanna M. Oksanen
Keyword(s):  
New Species ◽  
Membrane Vesicles ◽  
Virus Species ◽  
Virus Taxonomy ◽  
Dna Viruses ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Archaeal Viruses ◽  
The Family ◽  
Globally Distributed

AbstractEstablished in 2016, the family Pleolipoviridae comprises globally distributed archaeal viruses that produce pleomorphic particles. Pseudo-spherical enveloped virions of pleolipoviruses are membrane vesicles carrying a nucleic acid cargo. The cargo can be either a single-stranded or double-stranded DNA molecule, making this group the first family introduced in the 10th Report on Virus Taxonomy including both single-stranded and double-stranded DNA viruses. The length of the genomes is approximately 7–17 kilobase pairs, or kilonucleotides in the case of single-stranded molecules. The genomes are circular single-stranded DNA, circular double-stranded DNA, or linear double-stranded DNA molecules. Currently, eight virus species and seven proposed species are classified in three genera: Alphapleolipovirus (five species), Betapleolipovirus (nine species), and Gammapleolipovirus (one species). Here, we summarize the updated taxonomy of the family Pleolipoviridae to reflect recent advances in this field, with the focus on seven newly proposed species in the genus Betapleolipovirus: Betapleolipovirus HHPV3, HHPV4, HRPV9, HRPV10, HRPV11, HRPV12, and SNJ2.

scholarly journals vConTACT: an iVirus tool to classify double-stranded DNA viruses that infectArchaeaandBacteria

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3243 ◽  
Author(s):  
Benjamin Bolduc ◽  
Ho Bin Jang ◽  
Guilhem Doulcier ◽  
Zhi-Qiang You ◽  
Simon Roux ◽  
...  
Keyword(s):  
Sequence Space ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Double Stranded Dna ◽  
Microbial Ecosystems ◽  
Archaeal Viruses ◽  
Predictive Understanding ◽  
Taxonomic Assignments ◽  
User Friendly

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.

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 Hitchhiking of Viral Genomes on Cellular Chromosomes

2019 ◽  
Vol 6 (1) ◽  
pp. 275-296 ◽  
Author(s):  
Tami L. Coursey ◽  
Alison A. McBride
Keyword(s):  
Viral Genome ◽  
Viral Infections ◽  
Genome Replication ◽  
Mitotic Chromosomes ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Barr Virus ◽  
Dividing Cells ◽  
Viral Genome Replication ◽  
Epstein Barr

Persistent viral infections require a host cell reservoir that maintains functional copies of the viral genome. To this end, several DNA viruses maintain their genomes as extrachromosomal DNA minichromosomes in actively dividing cells. These viruses typically encode a viral protein that binds specifically to viral DNA genomes and tethers them to host mitotic chromosomes, thus enabling the viral genomes to hitchhike or piggyback into daughter cells. Viruses that use this tethering mechanism include papillomaviruses and the gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. This review describes the advantages and consequences of persistent extrachromosomal viral genome replication.

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 A pentameric protein ring with novel architecture is required for herpesviral packaging

2020 ◽  
Author(s):  
Allison L. Didychuk ◽  
Stephanie N. Gates ◽  
Matthew R. Gardner ◽  
Lisa M. Strong ◽  
Andreas Martin ◽  
...  
Keyword(s):  
Viral Genome ◽  
Molecular Motor ◽  
Dna Viruses ◽  
Dna Mutation ◽  
Viral Genomes ◽  
Barr Virus ◽  
Double Stranded Dna ◽  
Accessory Factor ◽  
Epstein Barr ◽  
Positively Charged

Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids. This process appears mechanistically similar in two evolutionarily distant viruses, the herpesviruses and the tailed bacteriophages, which infect different kingdoms of life. While the motor and mechanism as a whole are thought to be conserved, accessory factors that influence packaging are divergent and poorly understood, despite their essential roles. An accessory factor required for herpesviral packaging is encoded by ORF68 in the oncogenic virus Kaposi’s sarcoma-associated herpesvirus (KSHV), whose homolog in Epstein Barr Virus (EBV) is BFLF1. Here, we present structures of both KSHV ORF68 and EBV BFLF1, revealing that these proteins form a highly similar homopentameric ring. The central channel of this ring is positively charged, and we demonstrate that this region of KSHV ORF68 binds double-stranded DNA. Mutation of individual positively charged residues within but not outside the channel ablates DNA binding, and in the context of KSHV infection these mutants fail to package the viral genome or produce progeny virions. Thus, we propose a model in which ORF68 facilitates the transfer of newly replicated viral genomes to the packaging motor.

scholarly journals Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Disa Bäckström ◽  
Natalya Yutin ◽  
Steffen L. Jørgensen ◽  
Jennah Dharamshi ◽  
Felix Homa ◽  
...  
Keyword(s):  
Deep Sea ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Phylogenomic Analysis ◽  
Dna Viruses ◽  
Deep Sea Sediments ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Loki’S Castle ◽  
Virus Genomes

ABSTRACT The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome. IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

scholarly journals Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses

2015 ◽  
Vol 112 (38) ◽  
pp. E5318-E5326 ◽  
Author(s):  
Guillaume Blanc ◽  
Lucie Gallot-Lavallée ◽  
Florian Maumus
Keyword(s):  
Host Cell ◽  
Nuclear Genome ◽  
Eukaryotic Cell ◽  
Dna Viruses ◽  
Unicellular Eukaryotes ◽  
Indirect Control ◽  
Double Stranded Dna ◽  
Cell Mortality ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses

Virophages are recently discovered double-stranded DNA virus satellites that prey on giant viruses (nucleocytoplasmic large DNA viruses; NCLDVs), which are themselves parasites of unicellular eukaryotes. This coupled parasitism can result in the indirect control of eukaryotic cell mortality by virophages. However, the details of such tripartite relationships remain largely unexplored. We have discovered ∼300 predicted genes of putative virophage origin in the nuclear genome of the unicellular alga Bigelowiella natans. Physical clustering of these genes indicates that virophage genomes are integrated into the B. natans genome. Virophage inserts show high levels of similarity and synteny between each other, indicating that they are closely related. Virophage genes are transcribed not only in the sequenced B. natans strain but also in other Bigelowiella isolates, suggesting that transcriptionally active virophage inserts are widespread in Bigelowiella populations. Evidence that B. natans is also a host to NCLDV members is provided by the identification of NCLDV inserts in its genome. These putative large DNA viruses may be infected by B. natans virophages. We also identify four repeated elements sharing structural and genetic similarities with transpovirons—a class of mobile elements first discovered in giant viruses—that were probably independently inserted in the B. natans genome. We argue that endogenized provirophages may be beneficial to both the virophage and B. natans by (i) increasing the chances for the virophage to coinfect the host cell with an NCLDV prey and (ii) defending the host cell against fatal NCLDV infections.

scholarly journals Identification of Two Virus Integration Sites in the Brown Alga Feldmannia Chromosome

2007 ◽  
Vol 82 (3) ◽  
pp. 1407-1413 ◽  
Author(s):  
Russel H. Meints ◽  
Richard G. Ivey ◽  
Amy M. Lee ◽  
Tae-Jin Choi
Keyword(s):  
Vegetative Cells ◽  
Stem Loop ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Virus Particles ◽  
Double Stranded Dna ◽  
Stem Loop Structure ◽  
Integration Sites ◽  
Virus Integration ◽  
Cg Dinucleotide

ABSTRACT Two similar, large double-stranded DNA viruses, Feldmannia species virus 158 (FsV-158) and FsV-178, replicate only in the unilocular reproductive cells (sporangia) of a brown filamentous alga in the genus Feldmannia. Virus particles are not present in vegetative cells but they are produced in the sporangia formed on vegetative filaments that have been transferred newly into culture. Thus, we proposed that these viruses exist in the vegetative cells in a latent form (R. G. Ivey, E. C. Henry, A. M. Lee, L. Klepper, S. K. Krueger, and R. H. Meints, Virology 220:267-273, 1996). In this article we present evidence that the two FsV genomes are integrated into the host genome during vegetative growth. The FsV genome integration sites were identified by cloning the regions where the FsV genome is linked to the host DNA. FsV-158 and FsV-178 are integrated into two distinct locations in the algal genome. In contrast, the integration sites in the two viral genomes are identical. Notably, the integration sites in the host and viruses contain GC and CG dinucleotide sequences, respectively, from which the GC sequences are recovered at both host-virus junctions. The splice sites in the two FsV genomes are predicted to form a stem-loop structure with the CG dinucleotide in the loop portion.

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