A classification system for virophages and satellite viruses

Krupovìč, Mart; Kuhn, Jens H.; Fischer, Matthias

doi:10.1007/s00705-015-2622-9

Cited by 94 publications

(117 citation statements)

References 111 publications

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“…Among the 20–34 ORFs present in virophage genomes, six genes are conserved in most or all virophages and are considered as virophage core genes [48]. These six genes encode a MCP, a minor capsid protein (mCP), a putative FtsK-HerA family DNA packaging ATPase (ATPase), a cysteine protease (PRO), a DNA helicase/primase (S3H), and a zinc-ribbon domain containing protein (ZnR) encoded by a gene present in most, but not all, virophages (Figure 2) [48].…”

Section: Genomic Structure and Features Of Virophagesmentioning

confidence: 99%

“…These six genes encode a MCP, a minor capsid protein (mCP), a putative FtsK-HerA family DNA packaging ATPase (ATPase), a cysteine protease (PRO), a DNA helicase/primase (S3H), and a zinc-ribbon domain containing protein (ZnR) encoded by a gene present in most, but not all, virophages (Figure 2) [48]. In addition, in several virophages, the set of conserved genes encodes integrases of two different families (a putative tyrosine integrase found in Sputnik [17] and a putative rve integrase found in ALM and mavirus) [19,30].…”

Section: Genomic Structure and Features Of Virophagesmentioning

confidence: 99%

“…In addition, in several virophages, the set of conserved genes encodes integrases of two different families (a putative tyrosine integrase found in Sputnik [17] and a putative rve integrase found in ALM and mavirus) [19,30]. The existence of these core genes suggests a monophyletic origin for virophages, which supported the creation of a new viral family, named Lavidaviridae , for virophages, which includes Sputnik, Zamilon and mavirus isolates [48]. …”

Section: Genomic Structure and Features Of Virophagesmentioning

confidence: 99%

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The Expanding Family of Virophages

Bekliz

Colson

Scola

2016

Viruses

118

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Virophages replicate with giant viruses in the same eukaryotic cells. They are a major component of the specific mobilome of mimiviruses. Since their discovery in 2008, five other representatives have been isolated, 18 new genomes have been described, two of which being nearly completely sequenced, and they have been classified in a new viral family, Lavidaviridae. Virophages are small viruses with approximately 35–74 nm large icosahedral capsids and 17–29 kbp large double-stranded DNA genomes with 16–34 genes, among which a very small set is shared with giant viruses. Virophages have been isolated or detected in various locations and in a broad range of habitats worldwide, including the deep ocean and inland. Humans, therefore, could be commonly exposed to virophages, although currently limited evidence exists of their presence in humans based on serology and metagenomics. The distribution of virophages, the consequences of their infection and the interactions with their giant viral hosts within eukaryotic cells deserve further research.

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Section: Genomic Structure and Features Of Virophagesmentioning

confidence: 99%

Section: Genomic Structure and Features Of Virophagesmentioning

confidence: 99%

Section: Genomic Structure and Features Of Virophagesmentioning

confidence: 99%

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The Expanding Family of Virophages

Bekliz

Colson

Scola

2016

Viruses

118

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“…Most virophages also lack the DNAP gene but recently, a new group of putative virophages has been assembled from the sheep rumen metagenome and shown to encode a DNAP related to the polinton-encoded polymerases [26]. Although originally virophages were not considered full-fledged viruses, in recognition of their genuine viral nature, they were recently classified into a tentative family “ Lavidaviridae” [35]. …”

Section: Polintons Virophages Polinton-like Viruses: a Distinct Clamentioning

confidence: 99%

Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems

Krupovìč

Koonin

2016

Current Opinion in Microbiology

Self Cite

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Self-synthesizing transposons are the largest known transposable elements that encode their own DNA polymerases (DNAP). The Polinton/Maverick family of self-synthesizing transposons is widespread in eukaryotes and abundant in the genomes of some protists. In addition to the DNAP and a retrovirus-like integrase, most of the polintons encode homologs of the major and minor jelly-roll capsid proteins, DNA-packaging ATPase and capsid maturation protease. Therefore, polintons are predicted to alternate between the transposon and viral lifestyles although virion formation remains to be demonstrated. Polintons are related to a group of eukaryotic viruses known as virophages that parasitize on giant viruses of the family Mimiviridae and another recently identified putative family of polinton-like viruses (PLV) predicted to lead a similar, dual life style. Comparative genomic analysis of polintons, virophages, PLV and the other viruses with double-stranded (ds)DNA genomes infecting eukaryotes and prokaryotes suggests that the polintons evolved from bacterial tectiviruses and could have been the ancestors of a broad range of eukaryotic viruses including adenoviruses and members of the proposed order “Megavirales” as well as linear cytoplasmic plasmids. Recently, a group of predicted self-synthesizing transposons was discovered also in prokaryotes. These elements, denoted casposons, encode a DNAP and a homolog of the CRISPR-associated Cas1 endonuclease that has an integrase activity but no capsid proteins. Thus, unlike polintons, casposons appear to be limited to the transposon life style although they could have evolved from viruses. The casposons are thought to have played a pivotal role in the origin of the prokaryotic adaptive immunity, giving rise to the adaptation module of the CRISPR-Cas systems.

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“…The communication by Simmonds et al [41] addressed the classification of diverse groups of viral sequences derived from metagenomics approaches and this has resulted in significant changes in viral classification. For example, new families have been established to accommodate virophages and satellite viruses [23] and various novel groups of circular Rep encoding ssDNA viruses derived from environmental sources (with unknown hosts or pathology) [22,47,49]. In line with these significant changes on classification of viruses and viral-like elements, we communicate the establishment of a new family Alphasatellitidae with two sub-families Geminialphasatellitinae and Nanoalphasatellitinae for geminivirus-and nanovirus-alphasatellite molecules.…”

Section: Discussionmentioning

confidence: 84%

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

et al. 2018

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Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirusand nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.

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A classification system for virophages and satellite viruses

Cited by 94 publications

References 111 publications

The Expanding Family of Virophages

The Expanding Family of Virophages

Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

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