scholarly journals Evidence for a billion-years arms race between viruses, virophages and eukaryotes

2021 ◽  
Author(s):  
Jose Gabriel Nino Barreat ◽  
Aris Katzourakis
Keyword(s):  
Maximum Likelihood ◽  
Virus Particle ◽  
Arms Race ◽  
Linear Plasmids ◽  
Dna Viruses ◽  
Bayesian Hypothesis Testing ◽  
Phylogenetic Origin ◽  
Character Matrix ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Shed Light

The PRD1-adenovirus lineage is one of the oldest and most diverse lineages of viruses. In eukaryotes, they have diversified to an unprecedented extent giving rise to adenoviruses, virophages, Mavericks, Polinton-like viruses and Nucleocytoplasmic Large DNA viruses (NCLDVs) which include the poxviruses, asfarviruses and iridoviruses, among others. Two major hypotheses for their origins have been proposed: the 'virophage first' and 'nuclear escape' hypotheses, but their plausibility until now has remained unexplored. Here, we use maximum-likelihood and Bayesian hypothesis-testing to compare the two scenarios based on the shared proteins forming the virus particle and a comprehensive genomic character matrix. We also compare the phylogenetic origin of the transcriptional proteins shared by NCLDVs and cytoplasmic linear plasmids. Our analyses overwhelmingly favour the virophage first model. These findings shed light on one of the earliest diversifications seen in the virosphere, supporting a billion-years arms race between viruses, virophages and eukaryotes.

scholarly journals Transcriptome view of a killer: African swine fever virus

2020 ◽  
Vol 48 (4) ◽  
pp. 1569-1581 ◽  
Author(s):  
Gwenny Cackett ◽  
Michal Sýkora ◽  
Finn Werner
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Single Nucleotide ◽  
Dna Viruses ◽  
Temporal Regulation ◽  
Global Agriculture ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

African swine fever virus (ASFV) represents a severe threat to global agriculture with the world's domestic pig population reduced by a quarter following recent outbreaks in Europe and Asia. Like other nucleocytoplasmic large DNA viruses, ASFV encodes a transcription apparatus including a eukaryote-like RNA polymerase along with a combination of virus-specific, and host-related transcription factors homologous to the TATA-binding protein (TBP) and TFIIB. Despite its high impact, the molecular basis and temporal regulation of ASFV transcription is not well understood. Our lab recently applied deep sequencing approaches to characterise the viral transcriptome and gene expression during early and late ASFV infection. We have characterised the viral promoter elements and termination signatures, by mapping the RNA-5′ and RNA-3′ termini at single nucleotide resolution. In this review, we discuss the emerging field of ASFV transcripts, transcription, and transcriptomics.

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 The Old and the New on Viral Diseases in Sturgeon

Pathogens ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 146 ◽  
Author(s):  
Davide Mugetti ◽  
Paolo Pastorino ◽  
Vasco Menconi ◽  
Claudio Pedron ◽  
Marino Prearo
Keyword(s):  
Cell Culture ◽  
Infectious Diseases ◽  
Molecular Diagnosis ◽  
White Sturgeon ◽  
Viral Diseases ◽  
General Introduction ◽  
Dna Viruses ◽  
Cell Culture Isolation ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Few Data

Although sturgeon production by aquaculture has increased worldwide, a major factor limiting its expansion are infectious diseases, although few data about viral diseases are available however. This review provides a rapid overview of viral agents detected and described to date. Following a general introduction on viral diseases are four sections arranged by virus classification: sturgeon nucleocytoplasmic large DNA viruses, herpesviruses, white sturgeon adenovirus 1, and other viruses. Molecular diagnosis is currently the best tool to detect viral diseases, since cell culture isolation is not yet applicable for the detection of most sturgeon viruses.

scholarly journals Viral rhodopsins 1 are an unique family of light-gated cation channels

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Dmitrii Zabelskii ◽  
Alexey Alekseev ◽  
Kirill Kovalev ◽  
Vladan Rankovic ◽  
Taras Balandin ◽  
...  
Keyword(s):  
Phytoplankton Dynamics ◽  
Neural Firing ◽  
Dna Viruses ◽  
Carbon Cycles ◽  
Marine Food Chain ◽  
Conducting Pathway ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Ion Conducting ◽  
Unique Potential

Abstract Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that infect phytoplankton organisms and regulate the phytoplankton dynamics encompass genes of rhodopsins of two distinct families. Here, we present a functional and structural characterization of two proteins of viral rhodopsin group 1, OLPVR1 and VirChR1. Functional analysis of VirChR1 shows that it is a highly selective, Na+/K+-conducting channel and, in contrast to known cation channelrhodopsins, it is impermeable to Ca2+ ions. We show that, upon illumination, VirChR1 is able to drive neural firing. The 1.4 Å resolution structure of OLPVR1 reveals remarkable differences from the known channelrhodopsins and a unique ion-conducting pathway. Thus, viral rhodopsins 1 represent a unique, large group of light-gated channels (viral channelrhodopsins, VirChR1s). In nature, VirChR1s likely mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, might play a major role in global phytoplankton dynamics. Moreover, VirChR1s have unique potential for optogenetics as they lack possibly noxious Ca2+ permeability.

scholarly journals A55 Molecular systematics of sturgeon nucleocytoplasmic large DNA viruses

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
S Clouthier ◽  
E Anderson ◽  
G Kurath ◽  
R Breyta
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Small Subunit ◽  
Sequence Length ◽  
Dna Viruses ◽  
Mrna Capping ◽  
Capping Enzyme ◽  
Nucleocytoplasmic Large Dna Virus ◽  
Nucleocytoplasmic Large Dna Viruses

Abstract Namao virus (NV) is a sturgeon nucleocytoplasmic large DNA virus (sNCLDV) that can cause a lethal disease of the integumentary system in lake sturgeon Acipenser fulvescens. As a group, the sNCLDV have not been assigned to any currently recognized taxonomic family of viruses. In this study, a dataset of NV DNA sequences was generated and assembled as two non-overlapping contigs of 306 and 448 base pairs (bp) and then used to conduct a comprehensive systematics analysis using Bayesian phylogenetic inference for NV, other sNCLDV, and representative members of six families of the NCLDV superfamily. The phylogeny of NV was reconstructed using protein homologues encoded by nine nucleocytoplasmic virus orthologous genes (NCVOGs): NCVOG0022—mcp, NCVOG0038—DNA polymerase B elongation subunit, NCVOG0076—VV A18-type helicase, NCVOG0249—VV A32-type ATPase, NCVOG0262—AL2 VLTF3-like transcription factor, NCVOG0271—RNA polymerase II subunit II, NCVOG0274—RNA polymerase II subunit I, NCVOG0276—ribonucleotide reductase small subunit, and NCVOG1117—mRNA capping enzyme. The accuracy of our phylogenetic method was evaluated using a combination of Bayesian statistical analysis and congruence analysis. Stable tree topologies were obtained with datasets differing in target molecule(s), sequence length, and taxa. Congruent topologies were obtained in phylogenies constructed using individual protein datasets and when four proteins were used in a concatenated approach. The major capsid protein phylogeny indicated that ten representative sNCLDV form a monophyletic group comprised of four lineages within a polyphyletic Mimi-Phycodnaviridae group of taxa. Overall, the analyses revealed that Namao virus is a member of the Mimiviridae family with strong and consistent support for a clade containing NV and CroV as sister taxa.

scholarly journals Virus–Host Coevolution with a Focus on Animal and Human DNA Viruses

2019 ◽  
Vol 88 (1) ◽  
pp. 41-56 ◽  
Author(s):  
Győző L. Kaján ◽  
Andor Doszpoly ◽  
Zoltán László Tarján ◽  
Márton Z. Vidovszky ◽  
Tibor Papp
Keyword(s):  
Life Form ◽  
Eukaryotic Cell ◽  
Arms Race ◽  
Host Cells ◽  
Dna Viruses ◽  
Fitness Level ◽  
Cellular Life ◽  
Human Dna ◽  
Insight Into

Abstract Viruses have been infecting their host cells since the dawn of life, and this extremely long-term coevolution gave rise to some surprising consequences for the entire tree of life. It is hypothesised that viruses might have contributed to the formation of the first cellular life form, or that even the eukaryotic cell nucleus originates from an infection by a coated virus. The continuous struggle between viruses and their hosts to maintain at least a constant fitness level led to the development of an unceasing arms race, where weapons are often shuttled between the participants. In this literature review we try to give a short insight into some general consequences or traits of virus–host coevolution, and after this we zoom in to the viral clades of adenoviruses, herpesviruses, nucleo-cytoplasmic large DNA viruses, polyomaviruses and, finally, circoviruses.

scholarly journals Multiple evolutionary origins of giant viruses

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1840 ◽  
Author(s):  
Eugene V. Koonin ◽  
Natalya Yutin
Keyword(s):  
Life Forms ◽  
Translation System ◽  
Dna Viruses ◽  
Evolutionary Forces ◽  
Evolutionary Origins ◽  
Cellular Life ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Phylogenomic Analyses ◽  
Definition Of

The nucleocytoplasmic large DNA viruses (NCLDVs) are a monophyletic group of diverse eukaryotic viruses that reproduce primarily in the cytoplasm of the infected cells and include the largest viruses currently known: the giant mimiviruses, pandoraviruses, and pithoviruses. With virions measuring up to 1.5 μm and genomes of up to 2.5 Mb, the giant viruses break the now-outdated definition of a virus and extend deep into the genome size range typical of bacteria and archaea. Additionally, giant viruses encode multiple proteins that are universal among cellular life forms, particularly components of the translation system, the signature cellular molecular machinery. These findings triggered hypotheses on the origin of giant viruses from cells, likely of an extinct fourth domain of cellular life, via reductive evolution. However, phylogenomic analyses reveal a different picture, namely multiple origins of giant viruses from smaller NCLDVs via acquisition of multiple genes from the eukaryotic hosts and bacteria, along with gene duplication. Thus, with regard to their origin, the giant viruses do not appear to qualitatively differ from the rest of the virosphere. However, the evolutionary forces that led to the emergence of virus gigantism remain enigmatic.

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 Second Mitochondrial DNA Primase Is Essential for Cell Growth and Kinetoplast Minicircle DNA Replication in Trypanosoma brucei

2011 ◽  
Vol 10 (3) ◽  
pp. 445-454 ◽  
Author(s):  
Jane C. Hines ◽  
Dan S. Ray
Keyword(s):  
Mitochondrial Dna ◽  
Trypanosoma Brucei ◽  
Rna Recognition Motif ◽  
Dependent Manner ◽  
Dna Viruses ◽  
Content Type ◽  
Amino Terminal ◽  
Circular Dnas ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Minicircle Dna

ABSTRACT The mitochondrial DNA of trypanosomes contains two types of circular DNAs, minicircles and maxicircles. Both minicircles and maxicircles replicate from specific replication origins by unidirectional theta-type intermediates. Initiation of the minicircle leading strand and also that of at least the first Okazaki fragment involve RNA priming. The Trypanosoma brucei genome encodes two mitochondrial DNA primases, PRI1 and PRI2, related to the primases of eukaryotic nucleocytoplasmic large DNA viruses. These primases are members of the archeoeukaryotic primase superfamily, and each of them contain an RNA recognition motif and a PriCT-2 motif. In Leishmania species, PRI2 proteins are approximately 61 to 66 kDa in size, whereas in Trypanosoma species, PRI2 proteins have additional long amino-terminal extensions. RNA interference (RNAi) of T. brucei PRI2 resulted in the loss of kinetoplast DNA and accumulation of covalently closed free minicircles. Recombinant PRI2 lacking this extension (PRI2ΔNT) primes poly(dA) synthesis on a poly(dT) template in an ATP-dependent manner. Mutation of two conserved aspartate residues (PRI2ΔNTCS) resulted in loss of enzymatic activity but not loss of DNA binding. We propose that PRI2 is directly involved in initiating kinetoplast minicircle replication.

scholarly journals An Evolutionary View of the Arms Race between Protein Kinase R and Large DNA Viruses

2016 ◽  
Vol 90 (7) ◽  
pp. 3280-3283 ◽  
Author(s):  
Kathryn S. Carpentier ◽  
Adam P. Geballe
Keyword(s):  
Protein Kinase ◽  
Computational Methods ◽  
Experimental Models ◽  
Arms Race ◽  
Protein Kinase R ◽  
Arms Races ◽  
Dna Viruses ◽  
Evolutionary View ◽  
Cellular Defenses

To establish productive infections, viruses must counteract numerous cellular defenses that are poised to recognize viruses as nonself and to activate antiviral pathways. The opposing goals of host and viral factors lead to evolutionary arms races that can be illuminated by evolutionary and computational methods and tested in experimental models. Here we illustrate how this perspective has been contributing to our understanding of the interactions of the protein kinase R pathway with large DNA viruses.

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