Thirty-Thousand-Year-Old Distant Relative of Giant Icosahedral DNA Viruses with a Pandoravirus Morphology
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Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology Matthieu Legendrea,1, Julia Bartolia,1, Lyubov Shmakovab, Sandra Jeudya, Karine Labadiec, Annie Adraitd, Magali Lescota, Olivier Poirota, Lionel Bertauxa, Christophe Bruleyd, Yohann Coutéd, Elizaveta Rivkinab, Chantal Abergela,2, and Jean-Michel Claveriea,e,2 aStructural and Genomic Information Laboratory, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée) Centre National de la Recherche Scientifique, Aix–Marseille Université, 13288 Marseille Cedex 9, France; bInstitute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia; cCommissariat à l’Energie Atomique, Institut de Génomique, Centre National de Séquençage, 91057 Evry Cedex, France; dCommissariat à l’Energie Atomique, Institut de Recherches en Technologies et Sciences pour le Vivant, Biologie à Grande Echelle, Institut National de la Santé et de la Recherche Médicale, Unité 1038, Université Joseph Fourier Grenoble 1, 38054 Grenoble, France; and eAssistance Publique - Hopitaux de Marseille, 13385 Marseille, France Edited by James L. Van Etten, University of Nebraska–Lincoln, Lincoln, NE, and approved January 30, 2014 (received for review November 7, 2013) The largest known DNA viruses infect Acanthamoeba and belong larger amphora-shaped virions 1–1.2 μm in length. Their guanine– to two markedly different families. The Megaviridae exhibit cytosine (GC)-rich (>61%) genomes are up to 2.8 Mb long and pseudo-icosahedral virions up to 0.7 μm in diameter and adenine– encode up to 2,500 proteins sharing no resemblance with those of thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand Megaviridae (9). Finally, Pandoravirus particles do not incorporate proteins. Like their Mimivirus prototype discovered 10 y ago, they the transcription machinery that would allow them to entirely rep- entirely replicate within cytoplasmic virion factories. In contrast, the licate in the host’s cytoplasm. Known giant viruses infecting Acan- recently discovered Pandoraviruses exhibit larger amphora-shaped thamoeba were thus thought to belong to two very dissimilar types virions 1 μm in length and guanine–cytosine-rich genomes up to 2.8 in terms of particle structure, genome characteristics, and replica- Mb long encoding up to 2,500 proteins. Their replication involves the tionstrategies.Herewedescribeathirdtypeofgiantvirusnamed host nucleus. Whereas the Megaviridae share some general features “Pithovirus” (from the Greek word pithos designating the kind of MICROBIOLOGY with the previously described icosahedral large DNA viruses, the Pan- large amphora handed over by the gods to the legendary Pandora) doraviruses appear unrelated to them. Here we report the discovery propagating in an even larger pandoravirus-like particle, but of a third type of giant virus combining an even larger pandoravirus- exhibiting a replication cycle and genomic features reminiscent like particle 1.5 μminlengthwithasurprisinglysmaller600kbAT-rich of those of large icosahedral nucleocytoplasmic DNA viruses. genome, a gene content more similar to Iridoviruses and Marseillevi- Giant viruses are thus much more diverse than initially assumed. rus, and a fully cytoplasmic replication reminiscent of the Megaviri- dae. This suggests that pandoravirus-like particles may be associated Significance with a variety of virus families more diverse than previously envi- sioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated Giant DNA viruses are visible under a light microscope and a survey of the virome of Siberian permafrost. The revival of such an their genomes encode more proteins than some bacteria or ancestral amoeba-infecting virus used as a safe indicator of the pos- intracellular parasitic eukaryotes. There are two very distinct Acanthamoeba sible presence of pathogenic DNA viruses, suggests that the thawing types and infect unicellular protists such as .On of permafrost either from global warming or industrial exploitation one hand, Megaviridae possess large pseudoicosahedral capsids – of circumpolar regions might not be exempt from future threats to enclosing a megabase-sized adenine thymine-rich genome, and human or animal health. on the other, the recently discovered Pandoraviruses exhibit micron-sized amphora-shaped particles and guanine–cytosine- rich genomes of up to 2.8 Mb. While initiating a survey of the giant DNA virus | late Pleistocene | icosahedral capsid Siberian permafrost, we isolated a third type of giant virus com- bining the Pandoravirus morphology with a gene content more en years ago, the discovery of Acanthamoeba polyphaga similar to that of icosahedral DNA viruses. This suggests that TMimivirus revealed the existence of giant DNA viruses with pandoravirus-like particles may correspond to an unexplored di- particles large enough to be visible under a light microscope (1, 2). versity of unconventional DNA virus families. Further sampling of various environments and geographical loca- tions led to the isolation of Mimivirus variants (3, 4) and more Author contributions: C.A. and J.-M.C. designed research; M. Legendre, J.B., S.J., A.A., distant relatives, two of which have been fully sequenced: Mou- M. Lescot, L.B., C.A., and J.-M.C. performed research; K.L. performed DNA sequencing; mouvirus (5) and Megavirus chilensis (6). All of these viruses share L.S., K.L., C.B., Y.C., and E.R. contributed new reagents/analytic tools; M. Legendre, J.B., M. Lescot, O.P., Y.C., C.A., and J.-M.C. analyzed data; and M. Legendre, C.A., and J.-M.C. the same distinctive particle structure: a unique external fiber layer wrote the paper. μ enclosing a pseudoicosahedral protein capsid of about 0.5 min The authors declare no conflict of interest. diameter, itself containing lipid membranes surrounding an elec- This article is a PNAS Direct Submission. – tron-dense nucleocapsid. They share an adenine thymine (AT)-rich Data deposition: The Pithovirus genome sequence reported in this paper has been de- (>70%) linear DNA genome with sizes up to 1.26 Mb encoding up posited in GenBank database (accession no. KF740664). The MS proteomics data reported to 1,120 proteins (6). They all encode a full transcription apparatus in this paper have been deposited in the ProteomeXchange Consortium database, http:// ’ proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000460, via the Proteo- allowing them to replicate in the host s cytoplasm. These common mics Identifications database (www.ebi.ac.uk/pride/archive) partner repository [identifier features suggested that all giant viruses were to belong to a single no. PXD000460 (10.6019/PXD000460)]. family (Megaviridae) sharing the same particle morphology, geno- 1M. Legendre and J.B. contributed equally to this work. mic features, and replication strategy (7, 8). 2To whom correspondence may be addressed. E-mail: [email protected] or Chantal. This assumption was radically challenged by the discovery of [email protected]. Pandoraviruses (9), which show different and somewhat opposite This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. characteristics. These Acanthamoeba-infecting viruses exhibit much 1073/pnas.1320670111/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1320670111 PNAS Early Edition | 1of6 Downloaded by guest on September 24, 2021 ABC 100 nm D Fig. 1. Electron microscopy imaging of the Pith- ovirus replication cycle in A. castellanii.(A) Apex of the Pithovirus particle showing its unique cork made 100 nm 200 nm 100 nm of 15 nm-spaced stripes, rolled membranes un- derneath, and the internal membrane. (B)Two EF perpendicular views of the Pithovirus particles (cross- and longitudinal sections). The particles are wrapped intoa60nm-thickenvelopemadeof10nm-spaced parallel stripes. A lipid membrane is enclosing a ho- mogeneous interior where a tubular structure is seen N episodically, but in a reproducible fashion (arrow- VF head). (C)Topviewofthecorkrevealingahexagonal 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 G 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) 200 nm 2 µm 100 nm in the periphery of the virion factory (VF). These structures may contain preassembled particle build- ing blocks (Fig. S1). The cell nucleus (N) is visible. (G) HJI KInset highlighting a late stage of virion maturation with globular striated structures accumulating at the virion periphery. (H) Various stages of particle as- sembly 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 im- 200 nm 100 nm 200 nm 100 nm mature virion showing the envelope in the process of wrapping the particle. Results except for an electron-dense sphere (50 nm in diameter) seen Particle Morphology. If the notion that DNA may persist over episodically but in a reproducible fashion (Fig. S1)andatubular geological timespans (>1 My) is gaining