Diversity of virophages in metagenomic data sets

Journal of Virology

Volumn 87, Issue 8, 2013, Pages 4225-4236

  Zhou, Jinglie ^a,b,c   Zhang, Weijia ^b   Yan, Shuling ^d   Xiao, Jinzhou ^a,b   Zhang, Yuanyuan ^b,c   Li, Bailin ^a,b   Pan, Yingjie ^a,b   Wang, Yongjie ^b  

^a AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

^b SHANGHAI OCEAN UNIVERSITY   (China)

^c AUBURN UNIVERSITY   (United States)

^d UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; CAPSID PROTEIN; CYSTEINE PROTEINASE; MAJOR CAPSID PROTEIN; MINOR CAPSID PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL LINEAGE; CONTROLLED STUDY; DNA PACKAGING; GENE CLUSTER; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; METAGENOMICS; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; SPECIES DISTRIBUTION; SPECIES HABITAT; VIROPHAGE; VIRUS ASSEMBLY;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA VIRUSES; ENVIRONMENTAL MICROBIOLOGY; GENETIC VARIATION; GENOME, VIRAL; HUMANS; METAGENOME; OPEN READING FRAMES; PHYLOGEOGRAPHY; VIRAL PROTEINS;

ANIMALIA; DNA VIRUSES; MIRIDAE;

EID: 84875777180     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.03398-12     Document Type: Article

References (23)

1. Fischer MG, Suttle CA. 2011. A virophage at the origin of large DNA transposons. Science 332:231-234.
2. La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D. 2008. The virophage as a unique parasite of the giant mimivirus. Nature 455:100-104.
3. Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, Cavicchioli R. 2011. Virophage control of Antarctic algal host-virus dynamics. Proc. Natl. Acad. Sci. U. S. A. 108:6163-6168.
4. Sun S, La Scola B, Bowman VD, Ryan CM, Whitelegge JP, Raoult D, Rossmann MG. 2010. Structural studies of the Sputnik virophage. J. Virol. 84:894-897.
5. Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM. 2011. Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proc. Natl. Acad. Sci. U. S. A. 108:17486-17491.
6. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306:1344-1350.
7. Van Etten JL, Lane LC, Dunigan DD. 2010. DNA viruses: the really big ones (giruses). Annu. Rev. Microbiol. 64:83-99.
8. Claverie JM, Abergel C. 2009. Mimivirus and its virophage. Annu. Rev. Genet. 43:49-66.
9. Raoult D, Boyer M. 2010. Amoebae as genitors and reservoirs of giant viruses. Intervirology 53:321-329.
10. Fischer MG, Allen MJ, Wilson WH, Suttle CA. 2010. Giant virus with a remarkable complement of genes infects marine zooplankton. Proc. Natl. Acad. Sci. U. S. A. 107:19508-19513.
11. Dunigan DD, Fitzgerald LA, Van Etten JL. 2006. Phycodnaviruses: a peek at genetic diversity. Virus Res. 117:119-132.
12. Desnues C, La Scola B, Yutin N, Fournous G, Robert C, Azza S, Jardot P, Monteil S, Campocasso A, Koonin EV, Raoult D. 2012. Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc. Natl. Acad. Sci. U. S. A. 109:18078-18083.
13. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. 2011. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39:D546-D551.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
15. Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schaffer AA, Yu YK. 2005. Protein database searches using compositionally adjusted substitution matrices. FEBS J. 272:5101-5109.
16. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. doi:10 .1186/1471-2105-5-113.
17. Wang Y, Bininda-Emonds OR, van Oers MM, Vlak JM, Jehle JA. 2011. The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses. Virus Genes 42:444-456.
18. Wang Y, Kleespies RG, Huger AM, Jehle JA. 2007. The genome of Gryllus bimaculatus nudivirus indicates an ancient diversification of baculovirus-related nonoccluded nudiviruses of insects. J. Virol. 81:5395-5406.
19. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33:W116-W120.
20. Guindon S, Lethiec F, Duroux P, Gascuel O. 2005. PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33:W557-W559.
21. Parola P, Renvoise A, Botelho-Nevers E, La Scola B, Desnues C, Raoult D. 2012. Acanthamoeba polyphaga mimivirus virophage seroconversion in travelers returning from Laos. Emerg. Infect. Dis. 18:1500-1502.
22. Coolen MJL, Hopmans EC, Rijpstra WIC, Muyzer G, Schouten S, Volkman JK, Sinninghe Damsté JS. 2004. Evolution of the methane cycle in Ace Lake (Antarctica) during the Holocene: response of methanogens and methanotrophs to environmental change. Org. Geochem. 35:1151-1167.
23. Clingenpeel S, Macur RE, Kan J, Inskeep WP, Lovalvo D, Varley J, Mathur E, Nealson K, Gorby Y, Jiang H, LaFracois T, McDermott TR. 2011. Yellowstone Lake: high-energy geochemistry and rich bacterial diversity. Environ. Microbiol. 13:2172-2185.