iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

AbstractMicrobes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

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

Virus Evolution ◽

10.1093/ve/veaa008 ◽

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.

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Draft Genome Sequence of Sicyoidochytrium minutum DNA Virus Strain 001

Microbiology Resource Announcements ◽

10.1128/mra.00418-21 ◽

2021 ◽

Vol 10 (23) ◽

Author(s):

Yumi Murakoshi ◽

Takayuki Shimeki ◽

Daiske Honda ◽

Yoshitake Takao

Keyword(s):

Genome Sequence ◽

Virus Strain ◽

Draft Genome ◽

Draft Genome Sequence ◽

Dsdna Virus ◽

Dna Virus ◽

Coding Sequences ◽

Content Type ◽

Double Stranded Dna

Sicyoidochytrium minutum DNA virus strain 001 (SmDNAV 001) is a double-stranded DNA (dsDNA) virus that infects the marine fungoid protist Sicyoidochytrium minutum . We report the draft genome sequence of SmDNAV 001. The 236,345-bp genome contained 358 coding sequences (CDSs) and three tRNA-coding sequences.

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Temperature effects on virion volume and genome length in dsDNA viruses

Biology Letters ◽

10.1098/rsbl.2016.0023 ◽

2016 ◽

Vol 12 (3) ◽

pp. 20160023 ◽

Cited By ~ 2

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.

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Structure of faustovirus, a large dsDNA virus

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1523999113 ◽

2016 ◽

Vol 113 (22) ◽

pp. 6206-6211 ◽

Cited By ~ 47

Author(s):

Thomas Klose ◽

Dorine G. Reteno ◽

Samia Benamar ◽

Adam Hollerbach ◽

Philippe Colson ◽

...

Keyword(s):

Capsid Protein ◽

Major Capsid Protein ◽

Dsdna Virus ◽

Dna Virus ◽

Dna Viruses ◽

Double Stranded Dna ◽

Cryo Electron Microscopy ◽

Maturation Stages ◽

Jelly Roll ◽

Protein Shell

Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that has been found to use two protein shells to encapsidate and protect its genome. The crystal structure of the major capsid protein, in combination with cryo-electron microscopy structures of two different maturation stages of the virus, shows that the outer virus shell is composed of a double jelly-roll protein that can be found in many double-stranded DNA viruses. The structure of the repeating hexameric unit of the inner shell is different from all other known capsid proteins. In addition to the unique architecture, the region of the genome that encodes the major capsid protein stretches over 17,000 bp and contains a large number of introns and exons. This complexity might help the virus to rapidly adapt to new environments or hosts.

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Circular Double-Stranded Forms of TT Virus DNA in the Liver

Journal of Virology ◽

10.1128/jvi.74.11.5161-5167.2000 ◽

2000 ◽

Vol 74 (11) ◽

pp. 5161-5167 ◽

Cited By ~ 70

Author(s):

Hiroaki Okamoto ◽

Masato Ukita ◽

Tsutomu Nishizawa ◽

Junichi Kishimoto ◽

Yuji Hoshi ◽

...

Keyword(s):

Human Beings ◽

Specific Primer ◽

Dna Virus ◽

S1 Nuclease ◽

Tt Virus ◽

Double Stranded Dna ◽

Replicative Intermediates ◽

Paired Serum ◽

Genomic Length ◽

Liver Tissues

ABSTRACT TT virus (TTV) is an unenveloped, circular, and single-stranded DNA virus commonly infecting human beings worldwide. TTV DNAs in paired serum and liver tissues from three viremic individuals were separated by gel electrophoresis and characterized biophysically. TTV DNAs in sera migrated in sizes ranging from 2.0 to 2.5 kb. TTV DNAs in liver tissues, however, migrated at 2.0 to 2.5 kb as well as at 3.5 to 6.1 kb. Both faster- and slower-migrating forms of TTV DNAs in the liver were found to be circular and of the full genomic length of 3.8 kb. TTV DNAs migrating at 2.0 to 2.5 kb, from either serum or liver tissues, were sensitive to S1 nuclease but resistant to restriction endonucleases, and therefore, they were single-stranded. By contrast, TTV DNAs in liver tissues that migrated at 3.5 to 6.1 kb were resistant to S1 nuclease. They migrated at 3.7 to 4.0 kb after digestion with EcoRI, which suggests that they represent circular, double-stranded replicative intermediates of TTV. When TTV DNAs were subjected to strand-specific primer extension and then amplified by PCR with internal primers, those in serum were found to be minus-stranded DNAs while those in liver tissues were found to be a mixture of plus- and minus-stranded DNAs. These results suggest that TTV replicates in the liver via a circular double-stranded DNA.

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

Virus Evolution ◽

10.1093/ve/veaa055 ◽

2020 ◽

Cited By ~ 1

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.

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A Structural Model of the Genome Packaging Process in a Membrane-Containing Double Stranded DNA Virus

PLoS Biology ◽

10.1371/journal.pbio.1002024 ◽

2014 ◽

Vol 12 (12) ◽

pp. e1002024 ◽

Cited By ~ 24

Author(s):

Chuan Hong ◽

Hanna M. Oksanen ◽

Xiangan Liu ◽

Joanita Jakana ◽

Dennis H. Bamford ◽

...

Keyword(s):

Structural Model ◽

Genome Packaging ◽

Dna Virus ◽

Packaging Process ◽

Double Stranded Dna

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Virus-Specific Responses of Heterosigma akashiwo to Infection

Applied and Environmental Microbiology ◽

10.1128/aem.01207-06 ◽

2006 ◽

Vol 72 (12) ◽

pp. 7829-7834 ◽

Cited By ~ 24

Author(s):

Janice E. Lawrence ◽

Corina P. D. Brussaard ◽

Curtis A. Suttle

Keyword(s):

Viral Infection ◽

Rna Virus ◽

Geographic Area ◽

Heterosigma Akashiwo ◽

Dna Virus ◽

Cellular Physiology ◽

Sytox Green ◽

Double Stranded Dna ◽

Infected Cells

ABSTRACT We used flow cytometry to examine the process of cell death in the bloom-forming alga Heterosigma akashiwo during infection by a double-stranded DNA virus (OIs1) and a single-stranded RNA virus (H. akashiwo RNA virus [HaRNAV]). These viruses were isolated from the same geographic area and infect the same strain of H. akashiwo. By use of the live/dead stains fluorescein diacetate and SYTOX green as indicators of cellular physiology, cells infected with OIs1 showed signs of infection earlier than HaRNAV-infected cultures (6 to 17 h versus 23 to 29 h). Intracellular esterase activity was lost prior to increased membrane permeability during infection with OIs1, while the opposite was seen with HaRNAV-infected cultures. In addition, OIs1-infected cells accumulated in the cultures while HaRNAV-infected cells rapidly disintegrated. Progeny OIs1 viruses consisted of large and small morphotypes with estimated latent periods of 11 and 17 h, respectively, and about 1,100 and 16,000 viruses produced per cell, respectively. In contrast, HaRNAV produced about 21,000 viruses per cell and had a latent period of 29 h. This study reveals that the characteristics of viral infection in algae are virus dependent and therefore are variable among viruses infecting the same species. This is an important consideration for ecosystem modeling exercises; calculations based on in situ measurements of algal physiology must be sensitive to the diverse responses of algae to viral infection.

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Algal Viruses with Distinct Intraspecies Host Specificities Include Identical Intein Elements

Applied and Environmental Microbiology ◽

10.1128/aem.71.7.3599-3607.2005 ◽

2005 ◽

Vol 71 (7) ◽

pp. 3599-3607 ◽

Cited By ~ 50

Author(s):

Keizo Nagasaki ◽

Yoko Shirai ◽

Yuji Tomaru ◽

Kensho Nishida ◽

Shmuel Pietrokovski

Keyword(s):

Dna Polymerase ◽

Homing Endonuclease ◽

Sister Group ◽

Dna Virus ◽

Single Nucleotide Change ◽

Double Stranded Dna ◽

Endonuclease Domain ◽

Algal Viruses ◽

Molecular Phylogenetic ◽

Position Coding

ABSTRACT Heterosigma akashiwo virus (HaV) is a large double-stranded DNA virus infecting the single-cell bloom-forming raphidophyte (golden brown alga) H. akashiwo. A molecular phylogenetic sequence analysis of HaV DNA polymerase showed that it forms a sister group with Phycodnaviridae algal viruses. All 10 examined HaV strains, which had distinct intraspecies host specificities, included an intein (protein intron) in their DNA polymerase genes. The 232-amino-acid inteins differed from each other by no more than a single nucleotide change. All inteins were present at the same conserved position, coding for an active-site motif, which also includes inteins in mimivirus (a very large double-stranded DNA virus of amoebae) and in several archaeal DNA polymerase genes. The HaV intein is closely related to the mimivirus intein, and both are apparently monophyletic to the archaeal inteins. These observations suggest the occurrence of horizontal transfers of inteins between viruses of different families and between archaea and viruses and reveal that viruses might be reservoirs and intermediates in horizontal transmissions of inteins. The homing endonuclease domain of the HaV intein alleles is mostly deleted. The mechanism keeping their sequences basically identical in HaV strains specific for different hosts is yet unknown. One possibility is that rapid and local changes in the HaV genome change its host specificity. This is the first report of inteins found in viruses infecting eukaryotic algae.

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