Non-retroviral fossils in vertebrate genomes

Viruses

Volumn 3, Issue 10, 2011, Pages 1836-1848

  Horie, Masayuki ^a   Tomonaga, Keizo ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Endogenous non retroviral virus like elements; Exaptation; Non retroviral endogenization; Non retroviral integration; Viral fossil

Indexed keywords

DNA VIRUS LIKE ELEMENT; NON RETROVIRAL RNA VIRUS LIKE ELEMENT; NUCLEOPROTEIN; RT DNA VIRUS LIKE ELEMENT; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; VIRUS PROTEIN;

BORNA DISEASE VIRUS; CODON; DNA FLANKING REGION; DNA STRUCTURE; DNA VIRUS; ENDOGENOUS VIRUS; EVOLUTION; FILOVIRUS; FOSSIL; GENE LOCUS; GENOME; HEPADNAVIRUS; HUMAN; MIDWAYVIRUS; NON RETROVIRAL FOSSIL; NONHUMAN; NYAMANINIVIRUS; ORTHOLOGY; PARVOVIRUS; PHYLOGENETIC TREE; REVERSE TRANSCRIBING DNA VIRUS; REVIEW; RNA VIRUS; SYNTENY; TRANSCRIPTION REGULATION; VERTEBRATE; VIRUS DNA CELL DNA INTERACTION; VIRUS ENTRY;

ENDOGENOUS NON-RETROVIRAL VIRUS-LIKE ELEMENTS; EXAPTATION; NON-RETROVIRAL ENDOGENIZATION; NON-RETROVIRAL INTEGRATION; VIRAL FOSSIL;

ANIMALS; BORNAVIRIDAE; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME; HUMANS; MAMMALS; MONONEGAVIRALES INFECTIONS; RETROELEMENTS; VERTEBRATES; VIRUS INTEGRATION;

DNA VIRUSES; MAMMALIA; RNA VIRUSES; VERTEBRATA;

EID: 80055015143     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3101836     Document Type: Review

References (46)

1. Jern, P.; Coffin, J.M. Effects of retroviruses on host genome function. Annu. Rev. Genet. 2008, 42, 709-732.
2. Lander, E.S.; Linton, L.M.; Birren, B.; Nusbaum, C.; Zody, M.C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitz Hugh, W.; et al. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome. Nature 2001, 409, 860-921
3. Mouse Genome Sequencing Consortium; Waterston, R.H.; Lindblad-Toh, K.; Birney, E.; Rogers, J.; Abril, J.F.; Agarwal, P.; Agarwala, R.; Ainscough, R.; Alexandersson, M.; et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420, 520-562.
4. Stoye, J.P. Fv1, the mouse retrovirus resistance gene. Rev. Sci. Tech. 1998, 17, 269-277.
5. Mi, S.; Lee, X.; Li, X.; Veldman, G.M.; Finnerty, H.; Racie, L.; LaVallie, E.; Tang, X.Y.; Edouard, P.; Howes, S.; Keith, J.C., Jr.; McCoy, J.M. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 2000, 403, 785-789.
6. Blaise, S.; de Parseval, N.; Benit, L.; Heidmann, T. Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 13013-13018.
7. Dupressoir, A.; Marceau, G.; Vernochet, C.; Benit, L.; Kanellopoulos, C.; Sapin, V.; Heidmann, T. Syncytin-A and syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 725-730.
8. Dupressoir, A.; Vernochet, C.; Bawa, O.; Harper, F.; Pierron, G.; Opolon, P.; Heidmann, T. Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 12127-12132.
9. Zhdanov, V.M. Integration of viral genomes. Nature 1975, 256, 471-473.
10. Klenerman, P.; Hengartner, H.; Zinkernagel, R.M. A non-retroviral RNA virus persists in DNA form. Nature 1997, 390, 298-301.
11. Geuking, M.B.; Weber, J.; Dewannieux, M.; Gorelik, E.; Heidmann, T.; Hengartner, H.; Zinkernagel, R.M.; Hangartner, L. Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration. Science 2009, 323, 393-396.
12. Horie, M.; Honda, T.; Suzuki, Y.; Kobayashi, Y.; Daito, T.; Oshida, T.; Ikuta, K.; Jern, P.; Gojobori, T.; Coffin, J.M.; Tomonaga, K. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 2010, 463, 84-87.
13. Belyi, V.A.; Levine, A.J.; Skalka, A.M. Unexpected inheritance: Multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS Pathog. 2010, 6, e1001030.
14. Katzourakis, A.; Gifford, R.J. Endogenous viral elements in animal genomes. PLoS Genet. 2010, 6, e1001191.
15. Tomonaga, K.; Kobayashi, T.; Ikuta, K. Molecular and cellular biology of Borna disease virus infection. Microbes Infect. 2002, 4, 491-500.
16. Gonzalez-Dunia, D.; Cubitt, B.; de la Torre, J.C. Mechanism of Borna disease virus entry into cells. J. Virol. 1998, 72, 783-788.
17. Honda, T.; Horie, M.; Daito, T.; Ikuta, K.; Tomonaga, K. Molecular chaperone BiP interacts with Borna disease virus glycoprotein at the cell surface. J. Virol. 2009, 83, 12622-12625.
18. Clemente, R.; Sisman, E.; Aza-Blanc, P.; de la Torre, J.C. Identification of host factors involved in borna disease virus cell entry through a small interfering RNA functional genetic screen. J. Virol. 2010, 84, 3562-3575.
19. Taylor, D.J.; Leach, R.W.; Bruenn, J. Filoviruses are ancient and integrated into mammalian genomes. BMC Evol. Biol. 2010, 10, 193.
20. Watanabe, S.; Noda, T.; Kawaoka, Y. Functional mapping of the nucleoprotein of Ebola virus. J. Virol. 2006, 80, 3743-3751.
21. Shi, W.; Huang, Y.; Sutton-Smith, M.; Tissot, B.; Panico, M.; Morris, H.R.; Dell, A.; Haslam, S.M.; Boyington, J.; Graham, B.S.; Yang, Z.Y.; Nabel, G.J. A filovirus-unique region of Ebola virus nucleoprotein confers aberrant migration and mediates its incorporation into virions. J. Virol. 2008, 82, 6190-6199.
22. Mihindukulasuriya, K.A.; Nguyen, N.L.; Wu, G.; Huang, H.V.; da Rosa, A.P.; Popov, V.L.; Tesh, R.B.; Wang, D. Nyamanini and midway viruses define a novel taxon of RNA viruses in the order Mononegavirales. J. Virol. 2009, 83, 5109-5116.
23. de Lamballerie, X.; Crochu, S.; Billoir, F.; Neyts, J.; de Micco, P.; Holmes, E.C.; Gould, E.A. Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus. J. Gen. Virol. 2002, 83, 2443-2454.
24. Kobayashi, Y.; Horie, M.; Tomonaga, K.; Suzuki, Y. No evidence for natural selection on endogenous Borna-like nucleoprotein elements after divergence of Old World and New World monkeys. PLoS One 2011, 6, e24403.
25. Geib, T.; Sauder, C.; Venturelli, S.; Hassler, C.; Staeheli, P.; Schwemmle, M. Selective virus resistance conferred by expression of Borna disease virus nucleocapsid components. J. Virol. 2003, 77, 4283-4290.
26. Rauer, M.; Gotz, J.; Schuppli, D.; Staeheli, P.; Hausmann, J. Transgenic mice expressing the nucleoprotein of Borna disease virus in either neurons or astrocytes: Decreased susceptibility to homotypic infection and disease. J. Virol. 2004, 78, 3621-3632.
27. Ewing, R.M.; Chu, P.; Elisma, F.; Li, H.; Taylor, P.; Climie, S.; McBroom-Cerajewski, L.; Robinson, M.D.; O'Connor, L.; Li, M.; et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 2007, 3, 89.
28. Belyi, V.A.; Levine, A.J.; Skalka, A.M. Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: The parvoviridae and circoviridae are more than 40 to 50 million years old. J. Virol. 2010, 84, 12458-12462.
29. Kapoor, A.; Simmonds, P.; Lipkin, W.I. Discovery and characterization of mammalian endogenous parvoviruses. J. Virol. 2010, 84, 12628-12635.
30. Gilbert, C.; Feschotte, C. Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol. 2010, 8, e1000495.
31. Maestre, J.; Tchenio, T.; Dhellin, O.; Heidmann, T. MRNA retroposition in human cells: Processed pseudogene formation. EMBO J. 1995, 14, 6333-6338.
32. Esnault, C.; Maestre, J.; Heidmann, T. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 2000, 24, 363-367.
33. Feschotte, C. Virology: Bornavirus enters the genome. Nature 2010, 463, 39-40.
34. Tomonaga, K. Living fossil or evolving virus? EMBO Rep. 2010, 11, 327.
35. Ohshima, K.; Hattori, M.; Yada, T.; Gojobori, T.; Sakaki, Y.; Okada, N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol. 2003, 4, R74.
36. Smith, R.H. Adeno-associated virus integration: Virus versus vector. Gene Ther. 2008, 15, 817-822.
37. Miller, D.G.; Petek, L.M.; Russell, D.W. Adeno-associated virus vectors integrate at chromosome breakage sites. Nat. Genet. 2004, 36, 767-773.
38. Mehrle, S.; Rohde, V.; Schlehofer, J.R. Evidence of chromosomal integration of AAV DNA in human testis tissue. Virus Genes 2004, 28, 61-69.
39. Hendrie, P.C.; Hirata, R.K.; Russell, D.W. Chromosomal integration and homologous gene targeting by replication-incompetent vectors based on the autonomous parvovirus minute virus of mice. J. Virol. 2003, 77, 13136-13145.
40. Arbuckle, J.H.; Medveczky, M.M.; Luka, J.; Hadley, S.H.; Luegmayr, A.; Ablashi, D.; Lund, T.C.; Tolar, J.; De Meirleir, K.; Montoya, J.G.; Komaroff, A.L.; Ambros, P.F.; Medveczky, P.G. The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 5563-5568.
41. Daibata, M.; Taguchi, T.; Nemoto, Y.; Taguchi, H.; Miyoshi, I. Inheritance of chromosomally integrated human herpesvirus 6 DNA. Blood 1999, 94, 1545-1549.
42. Mori, T.; Tanaka-Taya, K.; Satoh, H.; Aisa, Y.; Yamazaki, R.; Kato, J.; Ikeda, Y.; Okamoto, S. Transmission of chromosomally integrated human herpesvirsus 6 (HHV-6) variant A from a parent to children leading to misdiagnosis of active HHV-6 infection. Transpl. Infect. Dis. 2009, 11, 503-506.
43. Bill, C.A.; Summers, J. Genomic DNA double-strand breaks are targets for hepadnaviral DNA integration. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 11135-11140.
44. Huang, J.M.; Huang, T.H.; Qiu, H.Y.; Fang, X.W.; Zhuang, T.G.; Liu, H.X.; Wang, Y.H.; Deng, L.Z.; Qiu, J.W. Effects of hepatitis B virus infection on human sperm chromosomes. World J. Gastroenterol. 2003, 9, 736-740.
45. Koonin, E.V. Taming of the shrewd: Novel eukaryotic genes from RNA viruses. BMC Biol. 2010, 8, 2.
46. Liu, H.; Fu, Y.; Jiang, D.; Li, G.; Xie, J.; Cheng, J.; Peng, Y.; Ghabrial, S.A.; Yi, X. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J. Virol. 2010, 84, 11876-11887.