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MIMIVIRE is a defence system in mimivirus that confers resistance to virophage

Abstract

Since their discovery, giant viruses have revealed several unique features that challenge the conventional definition of a virus, such as their large and complex genomes, their infection by virophages and their presence of transferable short element transpovirons1,2,3,4,5. Here we investigate the sensitivity of mimivirus to virophage infection in a collection of 59 viral strains and demonstrate lineage specificity in the resistance of mimivirus to Zamilon6, a unique virophage that can infect lineages B and C of mimivirus but not lineage A. We hypothesized that mimiviruses harbour a defence mechanism resembling the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system that is widely present in bacteria and archaea7,8,9,10. We performed de novo sequencing of 45 new mimivirus strains and searched for sequences specific to Zamilon in a total of 60 mimivirus genomes. We found that lineage A strains are resistant to Zamilon and contain the insertion of a repeated Zamilon sequence within an operon, here named the ‘mimivirus virophage resistance element’ (MIMIVIRE). Further analyses of the surrounding sequences showed that this locus is reminiscent of a defence mechanism related to the CRISPR–Cas system. Silencing the repeated sequence and the MIMIVIRE genes restores mimivirus susceptibility to Zamilon. The MIMIVIRE proteins possess the typical functions (nuclease and helicase) involved in the degradation of foreign nucleic acids. The viral defence system, MIMIVIRE, represents a nucleic-acid-based immunity against virophage infection.

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Figure 1: Chromosomal environment of the MIMIVIRE locus of Mimiviridae and virophage infection.

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Acknowledgements

We thank S. Benamar, A. Caputo and C. Robert for technical support, and L. Pinault for her assistance on protein production.

Author information

Authors and Affiliations

Authors

Contributions

A.L., B.L. and D.R. conceived the project and designed the study and experiments; A.L., M.B., P.P., B.L. and D.R. analysed the results; A.L. and D.R. wrote the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Bernard La Scola or Didier Raoult.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Histogram depicting the replication of Zamilon and Sputnik 3 DNA in Mimiviridae after its phylogenetic classification into lineages A, B and C.

The replication of each virophage was measured after 24 h using qPCR. The term Δ CT corresponds to the difference between the CT value specific to virophage at H0 and H24.

Extended Data Figure 2 The MIMIVIRE defence system.

a, A comparative model between prokaryotic CRISPR–Cas system and the viral MIMIVIRE system in APMV-A. b, The chromosomal environment of Mimiviridae lineage A is illustrated using mimivirus as an example. This organization is conserved across all APMV-A genomes. The 28-nucleotide-long Zamilon insert sequence is AATCTGATAATGAATCTGATAATGAATC, and the derived 15-nucleotide repeated unit is TGATAATGAATCTGA. The four repeats units are separated by 9, 48 and 63 nucleotides, respectively.

Extended Data Figure 3 Agarose gel electrophoresis of different DNA products treated with and without nuclease and/or helicase enzymes.

C, control; N, nuclease treatment for 2 h; H, helicase treatment for 2 h; H+N, helicase and nuclease treatment for 2 h; H*, helicase treatment for 2 h followed by heating at 94 °C for 10 min; H+N*, helicase and nuclease treatment for 2 h followed by heating at 94 °C for 10 min.

Extended Data Figure 4 Phylogenetic trees based on the sequences of the two Cas proteins.

a, R350. b, R354.

Extended Data Table 1 Identification of the Zamilon sequences that were found inserted into the 60 genomes of Mimiviridae
Extended Data Table 2 Functional inferences of the open reading frames in the vicinity of the MIMIVIRE locus in mimivirus

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-3. (PDF 156 kb)

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Levasseur, A., Bekliz, M., Chabrière, E. et al. MIMIVIRE is a defence system in mimivirus that confers resistance to virophage. Nature 531, 249–252 (2016). https://doi.org/10.1038/nature17146

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