RNA structural elements determine frequency and sites of nonhomologous recombination in an animal plus-strand RNA virus

Journal of Virology

Volumn 86, Issue 13, 2012, Pages 7393-7402

  Austermann Busch, Sophia ^a   Becher, Paul ^a  

^a UNIVERSITY OF VETERINARY MEDICINE HANNOVER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; BOVINE DIARRHEA VIRUS; CONTROLLED STUDY; DNA MODIFICATION; GENE FREQUENCY; GENE TARGETING; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA RECOMBINATION; RNA STRUCTURE; RNA TRANSPORT; RNA VIRUS; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS; VIRUS RECOMBINANT;

ANIMALS; BASE SEQUENCE; CATTLE; CELL LINE; DIARRHEA VIRUSES, BOVINE VIRAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RECOMBINATION, GENETIC; RNA, VIRAL; TRANSFECTION;

ANIMALIA; BOVINE VIRAL DIARRHEA VIRUS 1; FLAVIVIRIDAE; RNA VIRUSES;

EID: 84864139654     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.00864-12     Document Type: Article

References (57)

1. Arnold JJ, Cameron CE. 1999. Poliovirus RNA-dependent RNA polymerase (3Dpol) is sufficient for template switching in vitro. J. Biol. Chem. 274:2706 -2716.
2. Baroth M, Orlich M, Thiel HJ, Becher P. 2000. Insertion of cellular NEDD8 coding sequences in a pestivirus. Virology 278:456-466.
3. Becher P, Orlich M, König M, Thiel HJ. 1999. Nonhomologous RNA recombination in bovine viral diarrhea virus: molecular characterization of a variety of subgenomic RNAs isolated during an outbreak of fatal mucosal disease. J. Virol. 73:5646 -5653.
4. Becher P, et al. 1997. Phylogenetic analysis of pestiviruses from domestic and wild ruminants. J. Gen. Virol. 78(Pt 6):1357-1366.
5. Becher P, Orlich M, Thiel HJ. 1998. Ribosomal S27a coding sequences upstream of ubiquitin coding sequences in the genome of a pestivirus. J. Virol. 72:8697- 8704.
6. Becher P, Orlich M, Thiel HJ. 2001. RNA recombination between persisting pestivirus and a vaccine strain: generation of cytopathogenic virus and induction of lethal disease. J. Virol. 75:6256-6264.
7. Becher P, Tautz N. 2011. RNA recombination in pestiviruses: cellular RNA sequences in viral genomes highlight the role of host factors for viral persistence and lethal disease. RNA Biol. 8:216 -224.
8. Biebricher CK, Luce R. 1992. In vitro recombination and terminal elongation of RNA by Q beta replicase. EMBO J. 11:5129 -5135.
9. Bujarski JJ, Dzianott AM. 1991. Generation and analysis of nonhomologous RNA-RNA recombinants in brome mosaic virus: sequence complementarities at crossover sites. J. Virol. 65:4153- 4159.
10. Bujarski JJ, Kaesberg P. 1986. Genetic recombination between RNA components of a multipartite plant virus. Nature 321:528 -531.
11. Buzayan JM, Hampel A, Bruening G. 1986. Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res. 14:9729 -9743.
12. Cheng C-P, Nagy PD. 2003. Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNAdependent RNA polymerase in vitro. J. Virol. 77:12033-12047.
13. Cheng C-P, Serviene E, Nagy PD. 2006. Suppression of viral RNA recombination by a host exoribonuclease. J. Virol. 80:2631-2640.
14. Chetverin AB, Chetverina HV, Demidenko AA, Ugarov VI. 1997. Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure. Cell 88: 503-513.
15. Chetverin AB, Kopein DS, Chetverina HV, Demidenko AA, Ugarov VI. 2005. Viral RNA-directed RNA polymerases use diverse mechanisms to promote recombination between RNA molecules. J. Biol. Chem. 280: 8748-8755.
16. Chetverina HV, Demidenko AA, Ugarov VI, Chetverin AB. 1999. Spontaneous rearrangements in RNA sequences. FEBS Lett. 450:89 -94.
17. Chon SK, Perez DR, Donis RO. 1998. Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology 251:370- 382.
18. Devereux J, Haeberli P, Smithies O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
19. Filipowicz W, Konarska M, Gross HJ, Shatkin AJ. 1983. RNA 3=-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucleic Acids Res. 11:1405-1418.
20. Furuya T, Macnaughton TB, La Monica N, Lai MM. 1993. Natural evolution of coronavirus defective-interfering RNA involves RNA recombination. Virology 194:408-413.
21. Gallei A, et al. 2008. Cytopathogenicity of classical swine fever virus correlates with attenuation in the natural host. J. Virol. 82:9717-9729.
22. Gallei A, Pankraz A, Thiel H-J, Becher P. 2004. RNA recombination in vivo in the absence of viral replication. J. Virol. 78:6271- 6281.
23. Genschik P, Drabikowski K, Filipowicz W. 1998. Characterization of the Escherichia coli RNA 3=-terminal phosphate cyclase and its sigma54-regulated operon. J. Biol. Chem. 273:25516 -25526.
24. Gillespie JH, Baker JA, McEntee K. 1960. A cytopathogenic strain of virus diarrhea virus. Cornell Vet. 50:73-79.
25. Gmyl AP, et al. 1999. Nonreplicative RNA recombination in poliovirus. J. Virol. 73:8958-8965.
26. Gmyl AP, Korshenko SA, Belousov EV, Khitrina EV, Agol VI. 2003. Nonreplicative homologousRNArecombination: promiscuous joining of RNA pieces? RNA 9:1221-1231.
27. Gudima SO, Chang J, Taylor JM. 2005. Reconstitution in cultured cells of replicating HDV RNA from pairs of less than full-length RNAs. RNA 11:90 -98.
28. Hahn CS, Lustig S, Strauss EG, Strauss JH. 1988. Western equine encephalitis virus is a recombinant virus. Proc. Natl. Acad. Sci. U. S. A. 85:5997- 6001.
29. Holland J, et al. 1982. Rapid evolution of RNA genomes. Science 215: 1577-1585.
30. Isken O, Grassmann CW, Yu H, Behrens S-E. 2004. Complex signals in the genomic 3= nontranslated region of bovine viral diarrhea virus coordinate translation and replication of the viral RNA. RNA 10:1637-1652.
31. Jaag HM, Lu Q, Schmitt ME, Nagy PD. 2011. The role of ribonuclease MRP in viral RNA degradation and RNA recombination. J. Virol. 85:243- 253.
32. Jarvis TC, Kirkegaard K. 1992. Poliovirus RNA recombination: mechanistic studies in the absence of selection. EMBO J. 11:3135-3145.
33. Khatchikian D, Orlich M, Rott R. 1989. Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus. Nature 340:156 -157.
34. Kim MJ, Kao C. 2001. Factors regulating template switch in vitro by viral RNA-dependent RNA polymerases: implications for RNA-RNA recombination. Proc. Natl. Acad. Sci. U. S. A. 98:4972- 4977.
35. Lai MM. 1992. RNA recombination in animal and plant viruses. Microbiol. Rev. 56:61-79.
36. Lee KM, Gillespie JH. 1957. Propagation of virus diarrhea virus of cattle in tissue culture. Am. J. Vet. Res. 18:952-953.
37. Li WM, Barnes T, Lee CH. 2010. Endoribonucleases-enzymes gaining spotlight in mRNA metabolism. FEBS J. 277:627- 641.
38. Melton DA, et al. 1984. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 12:7035-7056.
39. Meyers G, Stoll D, Gunn M. 1998. Insertion of a sequence encoding light chain 3 of microtubule-associated proteins 1A and 1B in a pestivirus genome: connection with virus cytopathogenicity and induction of lethal disease in cattle. J. Virol. 72:4139-4148.
40. Meyers G, Tautz N, Becher P, Thiel HJ, Kümmerer BM. 1996. Recovery of cytopathogenic and noncytopathogenic bovine viral diarrhea viruses from cDNA constructs. J. Virol. 70:8606-8613.
41. Meyers G, et al. 1992. Rearrangement of viral sequences in cytopathogenic pestiviruses. Virology 191:368 -386.
42. Nagy PD, Bujarski JJ. 1997. Engineering of homologous recombination hotspots with AU-rich sequences in brome mosaic virus. J. Virol. 71: 3799-3810.
43. Nagy PD, Bujarski JJ. 1996. Homologous RNA recombination in brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers. J. Virol. 70:415- 426.
44. Pankraz A, Thiel H-J, Becher P. 2005. Essential and nonessential elements in the 3= nontranslated region of bovine viral diarrhea virus. J. Virol. 79:9119 -9127.
45. Poole TL, et al. 1995. Pestivirus translation initiation occurs by internal ribosome entry. Virology 206:750 -754.
46. Qi F, Ridpath JF, Lewis T, Bolin SR, Berry ES. 1992. Analysis of the bovine viral diarrhea virus genome for possible cellular insertions. Virology 189:285-292.
47. Schlesinger S, Weiss BG. 1994. Recombination between Sindbis virus RNAs. Arch. Virol. Suppl. 9:213-220.
48. Shapka N, Nagy PD. 2004. The AU-rich RNA recombination hot spot sequence of brome mosaic virus is functional in tombusviruses: implications for the mechanism of RNA recombination. J. Virol. 78:2288 -2300.
49. Simmonds P, et al. 2011. Family Flaviviridae, p 1003-1020. In King A, Lefkowitz E, Adams MJ, Carstens EB (ed), Virus taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA.
50. Steinschneider A, Fraenkel-Conrat H. 1966. Studies of nucleotide sequences in tobacco mosaic virus ribonucleic acid. 3. Periodate oxidation and semicarbazone formation. Biochemistry 5:2729 -2734.
51. Steinschneider A, Fraenkel-Conrat H. 1966. Studies of nucleotide sequences in tobacco mosaic virus ribonucleic acid. IV. Use of aniline in stepwise degradation. Biochemistry 5:2735-2743.
52. Suzuki Y, Gojobori T, Nakagomi O. 1998. Intragenic recombinations in rotaviruses. FEBS Lett. 427:183-187.
53. Tautz N, Meyers G, Stark R, Dubovi EJ, Thiel HJ. 1996. Cytopathogenicity of a pestivirus correlates with a 27-nucleotide insertion. J. Virol. 70:7851-7858.
54. Tautz N, Thiel HJ, Dubovi EJ, Meyers G. 1994. Pathogenesis of mucosal disease: a cytopathogenic pestivirus generated by an internal deletion. J. Virol. 68:3289 -3297.
55. Vilcek S, et al. 1994. Pestiviruses isolated from pigs, cattle and sheep can be allocated into at least three genogroups using polymerase chain reaction and restriction endonuclease analysis. Arch. Virol. 136:309 - 323.
56. Walter JE, et al. 2001. Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children. Arch. Virol. 146:2357-2367.
57. Yu H, Grassmann CW, Behrens SE. 1999. Sequence and structural elements at the 3= terminus of bovine viral diarrhea virus genomic RNA: functional role during RNA replication. J. Virol. 73:3638 -3648.