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. 2014 Mar 18;111(11):4274-9.
doi: 10.1073/pnas.1320670111. Epub 2014 Mar 3.

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

Matthieu Legendre  1 , Julia Bartoli, Lyubov Shmakova, Sandra Jeudy, Karine Labadie, Annie Adrait, Magali Lescot, Olivier Poirot, Lionel Bertaux, Christophe Bruley, Yohann Couté, Elizaveta Rivkina, Chantal Abergel, Jean-Michel Claverie
Affiliations

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

Matthieu Legendre et al. Proc Natl Acad Sci U S A. .

Abstract

The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine-thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine-cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health.

Keywords: giant DNA virus; icosahedral capsid; late Pleistocene.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Electron microscopy imaging of the Pithovirus replication cycle in A. castellanii. (A) Apex of the Pithovirus particle showing its unique cork made of 15 nm-spaced stripes, rolled membranes underneath, and the internal membrane. (B) Two perpendicular views of the Pithovirus particles (cross- and longitudinal sections). The particles are wrapped into a 60 nm-thick envelope made of 10 nm-spaced parallel stripes. A lipid membrane is enclosing a homogeneous interior where a tubular structure is seen episodically, but in a reproducible fashion (arrowhead). (C) Top view of the cork revealing a hexagonal honeycomb-like array. (D) Bottom view of the particle showing the striated organization of the envelope. (E) An opened Pithovirus particle in the host vacuole. Parts of the expelled cork are visible (black arrows) and the internal membrane of the particle (black arrowhead) appears ready to fuse with the vacuole membrane. (F) Maturing virions at a late stage of infection. Structures made of stripes, pieces of cork, and dense material accumulate (white arrowhead) in the periphery of the virion factory (VF). These structures may contain preassembled particle building blocks (Fig. S1). The cell nucleus (N) is visible. (G) Inset highlighting a late stage of virion maturation with globular striated structures accumulating at the virion periphery. (H) Various stages of particle assembly in the same cell. (I) Incompletely assembled rectangular particle lacking its thick envelope. The striated cork is already visible. (J) At a later stage, the particle adopts its final rounded shape while its envelope thickens. (K) Orthogonal view of an immature virion showing the envelope in the process of wrapping the particle.
Fig. 2.
Fig. 2.
Distributions of the Pithovirus protein closest homologs. (A) All predicted protein sequences against the NCBI NR (non-redundant) database. (B) Distribution of the 51 best-matching viral proteins. (C) Subset of the 159 proteins detected in the particle proteome. (D) Distribution of the predicted protein functions.
Fig. 3.
Fig. 3.
Distribution, structure, and expression of Pithovirus genome repeats. (A) Alignment (dot-plot) of the Pithovirus genome nucleotide sequence against itself. Repeated sequences appear as a black patchwork. The x axis shows genomic position and the y axis shows the gene position. The upper part of the figure shows the distribution of genes on the forward strand (red) and reverse strand (blue). (B) Enlarged view on one of the repeat-containing regions. Each cross is characteristic of a palindromic sequence whereas parallel lines indicate tandem repeated sequences. Notice that each palindromic sequence is itself repeated multiple times. (C) Sequence logo showing the sequence conservation of the palindromic repeats. (D) The transcription level assigned to each genome position is defined as its coverage by RNA-seq reads. The repeat regions are the least expressed.
Fig. 4.
Fig. 4.
Clustering of viral and eukaryotic DNA polymerases. A multiple alignment of 57 eukaryotic and large virus DNA polymerase sequences (569 ungapped positions) was computed using the default options of the MAFFT server (40). The neighbor-joining tree was built using the JTT substitution model (estimated α = 1.05) and 100 bootstrap resamplings were performed. The tree was rooted at the basis of the eukaryotes and collapsed for bootstrap values <50 before drawing using MEGA5 (41). The Pithovirus DNA polymerase sequence (red) does not cluster with the Pandoraviruses (purple), but falls within a clade clustering the Iridoviruses and Marseilleviruses (orange). Other colors are used to distinguish eukaryotes (turquoise) and viruses from different families: Megaviridae (green), Phycodnaviridae (blue), Herpesviridae (dark gray), Baculoviridae (light gray), Asfar (black), and Poxviridae (gray).
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References

    1. La Scola B, et al. A giant virus in amoebae. Science. 2003;299(5615):2033. - PubMed
    1. Raoult D, et al. The 1.2-megabase genome sequence of Mimivirus. Science. 2004;306(5700):1344–1350. - PubMed
    1. Colson P, et al. Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes. Genome Biol Evol. 2011;3:737–742. - PMC - PubMed
    1. Desnues C, et al. Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci USA. 2012;109(44):18078–18083. - PMC - PubMed
    1. Yoosuf N, et al. Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage. Genome Biol Evol. 2012;4(12):1324–1330. - PMC - PubMed

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