In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba

Matthieu Legendre; Audrey Lartigue; Lionel Bertaux; Sandra Jeudy; Julia Bartoli; Magali Lescot; Jean-Marie Alempic; Claire Ramus; Christophe Bruley; Karine Labadie; Lyubov Shmakova; Elizaveta Rivkina; Yohann Couté; Chantal Abergel; Jean-Michel Claverie

doi:10.1073/pnas.1510795112

New Research In

Edited by James L. Van Etten, University of Nebraska, Lincoln, NE, and approved August 12, 2015 (received for review June 2, 2015)

Significance

The saga of giant viruses (i.e. visible by light microscopy) started in 2003 with the discovery of Mimivirus. Two additional types of giant viruses infecting Acanthamoeba have been discovered since: the Pandoraviruses (2013) and Pithovirus sibericum (2014), the latter one revived from 30,000-y-old Siberian permafrost. We now describe Mollivirus sibericum, a fourth type of giant virus isolated from the same permafrost sample. These four types of giant virus exhibit different virion structures, sizes (0.6–1.5 µm), genome length (0.6–2.8 Mb), and replication cycles. Their origin and mode of evolution are the subject of conflicting hypotheses. The fact that two different viruses could be easily revived from prehistoric permafrost should be of concern in a context of global warming.

Abstract

Acanthamoeba species are infected by the largest known DNA viruses. These include icosahedral Mimiviruses, amphora-shaped Pandoraviruses, and Pithovirus sibericum, the latter one isolated from 30,000-y-old permafrost. Mollivirus sibericum, a fourth type of giant virus, was isolated from the same permafrost sample. Its approximately spherical virion (0.6-µm diameter) encloses a 651-kb GC-rich genome encoding 523 proteins of which 64% are ORFans; 16% have their closest homolog in Pandoraviruses and 10% in Acanthamoeba castellanii probably through horizontal gene transfer. The Mollivirus nucleocytoplasmic replication cycle was analyzed using a combination of “omic” approaches that revealed how the virus highjacks its host machinery to actively replicate. Surprisingly, the host’s ribosomal proteins are packaged in the virion. Metagenomic analysis of the permafrost sample uncovered the presence of both viruses, yet in very low amount. The fact that two different viruses retain their infectivity in prehistorical permafrost layers should be of concern in a context of global warming. Giant viruses’ diversity remains to be fully explored.

Footnotes

↵¹M. Legendre and A.L. contributed equally to this work.
↵²Present address: Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Unité Mixte de Recherche 7255 (Institut de Microbiologie de la Méditerranée, FR3479) Centre National de la Recherche Scientifique, Aix-Marseille Université, 13009 Marseille, France.
↵³To whom correspondence may be addressed. Email: Chantal.Abergel{at}igs.cnrs-mrs.fr, jean-michel.claverie{at}univ-amu.fr.

Author contributions: Y.C., C.A., and J.-M.C. designed research; M. Legendre, A.L., L.B., S.J., J.B., M. Lescot, J.-M.A., C.R., Y.C., C.A., and J.-M.C. performed research; K.L. performed sequencing; A.L., C.R., C.B., K.L., L.S., E.R., and Y.C. contributed new reagents/analytic tools; M. Legendre, A.L., M. Lescot, Y.C., C.A., and J.-M.C. analyzed data; M. Legendre, C.A., and J.-M.C. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The Mollivirus genome sequence reported in this paper has been deposited in the GenBank database (accession no. KR921745). The transcriptomic data have been deposited in the Sequence Read Archive, www.ncbi.nlm.nih.gov/Traces/sra/ [accession no. SRX1078581 (SRR2084123 for the early class of expression, SRR2103267 for the intermediate one, and SRR2103268 for the late class of expression)]. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium, proteomecentral.proteomexchange.org, via the Proteomics Identifications partner repository [dataset identifiers <PXD002375> (Particule and Surfome) and <PXD002374> (Time Course)]. All data can be visualized on an interactive genome browser at the following link: www.igs.cnrs-mrs.fr/cgi-bin/gb2/gbrowse/Mollivirus/.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1510795112/-/DCSupplemental.