Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 6, 2012, Pages 1907-1912

  Routh, Andrew ^a   Domitrovic, Tatiana ^a   Johnson, John E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Deep sequencing; Virus assembly; Virus evolution

Indexed keywords

BACULOVIRUS VECTOR; MESSENGER RNA; RIBOSOME RNA; SINGLE STRANDED RNA; UNTRANSLATED RNA;

ARTICLE; EUKARYOTE; EXPRESSION VECTOR; HERD; HORIZONTAL GENE TRANSFER; HOST; HUMAN; MUTATION; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA VIRUS; TRANSPOSON; VIRION; VIRUS GENOME; VIRUS PARTICLE; VIRUS VIRULENCE;

ANIMALS; CAPSID; CELL LINE; DNA TRANSPOSABLE ELEMENTS; EUKARYOTA; GENE EXPRESSION REGULATION, VIRAL; GENOME, VIRAL; HOST-PATHOGEN INTERACTIONS; MUTATION RATE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA VIRUSES; RNA, MESSENGER; RNA, VIRAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; VIRION; VIRUS ASSEMBLY;

EUKARYOTA; FLOCK HOUSE VIRUS; NUDAURELIA CAPENSIS OMEGA VIRUS; RNA VIRUSES;

EID: 84863181640     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1116168109     Document Type: Article

References (44)

1. Wright CF, et al. (2011) Beyond the consensus: Dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. J Virol 85:2266-2275.
2. Cordey S, et al. (2010) Rhinovirus genome evolution during experimental human infection. PLoS One 5:e10588.
3. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance. Genome Res 17:1195-1201. (Pubitemid 47204863)
4. Victoria JG, et al. (2010) Viral nucleic acids in live-attenuated vaccines: Detection of minority variants and an adventitious virus. J Virol 84:6033-6040.
5. Nakamura S, et al. (2009) Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 4:e4219.
6. Feng H, Shuda M, Chang Y, Moore PS (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:1096-1100. (Pubitemid 351300792)
7. Wu Q, et al. (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA 107:1606-1611.
8. Tsai B (2007) Penetration of nonenveloped viruses into the cytoplasm. Annu Rev Cell Dev Biol 23:23-43.
9. Odegard A, Banerjee M, Johnson JE (2010) Flock house virus: A model system for understanding nonenveloped virus entry and membrane penetration. Curr Top Microbiol Immunol 343:1-22.
10. Banerjee M, Johnson JE (2008) Activation, exposure and penetration of virally encoded, membrane-active polypeptides during nonenveloped virus entry. Curr Protein Pept Sci 9:16-27.
11. Krishna NK, Schneemann A (1999) Formation of an RNA heterodimer upon heating of nodavirus particles. J Virol 73:1699-1703. (Pubitemid 29036833)
12. Hanzlik TN, Gordon KH (1997) The Tetraviridae. Adv Virus Res 48:101-168.
13. Canady MA, Tihova M, Hanzlik TN, Johnson JE, Yeager M (2000) Large conformational changes in the maturation of a simple RNA virus, Nudaurelia capensis omega virus (NωV). J Mol Biol 299:573-584.
14. Fisher AJ, Johnson JE (1993) Ordered duplex RNA controls capsid architecture in an icosahedral animal virus. Nature 361:176-179. (Pubitemid 23031355)
15. Schneemann A, Zhong W, Gallagher TM, Rueckert RR (1992) Maturation cleavage required for infectivity of a nodavirus. J Virol 66:6728-6734.
16. Schneemann A, Dasgupta R, Johnson JE, Rueckert RR (1993) Use of recombinant baculoviruses in synthesis of morphologically distinct virus-like particles of flock house virus, a nodavirus. J Virol 67:2756-2763. (Pubitemid 23118874)
17. Agrawal DK, Johnson JE (1995) Assembly of the T = 4 Nudaurelia capensis omega virus capsid protein, posttranslational cleavage, and specific encapsidation of its mRNA in a baculovirus expression system. Virology 207:89-97.
18. Kazazian HH, Jr (1998) Mobile elements and disease. Curr Opin Genet Dev 8:343-350.
19. Negre V, et al. (2006) SPODOBASE: An EST database for the lepidopteran crop pest Spodoptera. BMC Bioinf 7:322.
20. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-829. (Pubitemid 351645072)
21. Arias RS, Blanco CA, Portilla M, Snodgrass GL, Scheffler BE (2011) First microsatellites from Spodoptera frugiperda (Lepidoptera: Noctuidae) and their potential use for population genetics. Ann Entomol Soc Am 104:576-587.
22. Xiong Y, Eickbush TH (1988) The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons. Mol Cell Biol 8:114-123.
23. Jakubczak JL, Zenni MK, Woodruff RC, Eickbush TH (1992) Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Genetics 131:129-142.
24. Jamrich M, Miller OL, Jr (1984) The rare transcripts of interrupted rRNA genes in Drosophila melanogaster are processed or degraded during synthesis. EMBO J 3:1541-1545.
25. Ye J, Eickbush TH (2006) Chromatin structure and transcription of the R1- and R2- inserted rRNA genes of Drosophila melanogaster. Mol Cell Biol 26:8781-8790. (Pubitemid 44851938)
26. Li TC, Scotti PD, Miyamura T, Takeda N (2007) Latent infection of a new alpha-nodavirus in an insect cell line. J Virol 81:10890-10896. (Pubitemid 47536063)
27. Kaminker JS, et al. (2002) The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective. Genome Biol 3, 10.1186/gb-2002-3-12-research0084.
28. Di Franco C, Pisano C, Fourcade-Peronnet F, Echalier G, Junakovic N (1992) Evidence for de novo rearrangements of Drosophila transposable elements induced by the passage to the cell culture. Genetica 87:65-73.
29. Giles KE, Caputi M, Beemon KL (2004) Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes. RNA 10:299-307. (Pubitemid 38129834)
30. Onafuwa-Nuga AA, Telesnitsky A, King SR (2006) 7SL RNA, but not the 54-kd signal recognition particle protein, is an abundant component of both infectious HIV-1 and minimal virus-like particles. RNA 12:542-546.
31. Lanman J, et al. (2008) Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy. J Struct Biol 161:439-446. (Pubitemid 351375095)
32. Freistadt MS, Vaccaro JA, Eberle KE (2007) Biochemical characterization of the fidelity of poliovirus RNA-dependent RNA polymerase. Virol J 4:44.
33. Malik HS, Henikoff S, Eickbush TH (2000) Poised for contagion: Evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res 10:1307-1318.
34. Silva JC, Loreto EL, Clark JB (2004) Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol 6:57-71.
35. Jordan IK, Matyunina LV, McDonald JF (1999) Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc Natl Acad Sci USA 96:12621-12625. (Pubitemid 29513552)
36. Diao X, Freeling M, Lisch D (2006) Horizontal transfer of a plant transposon. PLoS Biol 4:e5.
37. Gilbert C, Schaack S, Pace JK, 2nd, Brindley PJ, Feschotte C (2010) A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464:1347-1350.
38. Pace JK, 2nd, Gilbert C, Clark MS, Feschotte C (2008) Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci USA 105:17023-17028.
39. Lecher P, Bucheton A, Pelisson A (1997) Expression of the Drosophila retrovirus gypsy as ultrastructurally detectable particles in the ovaries of flies carrying a permissive flamenco allele. J Gen Virol 78:2379-2388. (Pubitemid 27387054)
40. Piskurek O, Okada N (2007) Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc Natl Acad Sci USA 104:12046-12051. (Pubitemid 47185627)
41. Friesen PD, Nissen MS (1990) Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome. Mol Cell Biol 10:3067-3077.
42. Jehle JA, Nickel A, Vlak JM, Backhaus H (1998) Horizontal escape of the novel Tc1-like lepidopteran transposon TCp3.2 into Cydia pomonella granulovirus. J Mol Evol 46:215-224. (Pubitemid 28079945)
43. Schneemann A, Marshall D (1998) Specific encapsidation of nodavirus RNAs is mediated through the C terminus of capsid precursor protein alpha. J Virol 72:8738-8746. (Pubitemid 28471816)
44. Xu G, et al. (2011) SAMMate: A GUI tool for processing short read alignments in SAM/ BAM format. Source Code Biol Med 6:2.