Efficient in vitro system of homologous recombination in brome mosaic bromovirus

Journal of Virology

Volumn 80, Issue 12, 2006, Pages 6182-6187

  Wierzchoslawski, Rafal ^a,c   Bujarski, Jozef J ^a,b  

^a NORTHERN ILLINOIS UNIVERSITY   (United States)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RECOMBINANT PROTEIN; RECOMBINASE;

AMINO ACID SUBSTITUTION; ARTICLE; BROMOVIRUS; DNA TEMPLATE; GENE SEQUENCE; IN VITRO STUDY; LIFE CYCLE; MOSAIC VIRUS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA RECOMBINATION; RNA SYNTHESIS; VIRUS GENOME; VIRUS RECOMBINATION; VIRUS REPLICATION;

BROMOVIRUS; CELL-FREE SYSTEM; CYSTEINE ENDOPEPTIDASES; PROMOTER REGIONS (GENETICS); RECOMBINATION, GENETIC; RNA REPLICASE; TEMPLATES, GENETIC;

BROME MOSAIC VIRUS; BROMOVIRUS; BROMUS;

EID: 33744910313     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.02447-05     Document Type: Article

References (60)

1. Aaziz, R., and M. Tepfer. 1999. Recombination between genomic RNAs of two cucumoviruses under conditions of minimal selection pressure. Virology 263:282-289.
2. Adair, T. L., and C. M. Kearney. 2000. Recombination between a 3-kilobase tobacco mosaic virus transgene and a homologous viral construct in the restoration of viral and nonviral genes. Arch. Virol. 145:1867-1883.
3. pol) is sufficient for template switching in vitro. J. Biol. Chem. 274:2706-2716.
4. Barr, J. N., and G. W. Wertz. 2001. Polymerase slippage at vesicular stomatitis virus gene junctions to generate poly(A) is regulated by the upstream 3′-AUAC-5′ tetranucleotide: implications for the mechanism of transcription termination. J. Virol. 75:6901-6913.
5. Baumstark, T., and P. Ahlquist. 2001. The brome mosaic virus RNA3 intergenic replication enhancer folds to mimic a tRNA TpsiC-stem loop and is modified in vivo. RNA 7:1652-1670.
6. Becher, P., M. Orlich, and H. J. Thiel. 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. Bousalem, M., E. J. Douzery, and D. Fargette. 2000. High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of yam mosaic virus: a contribution to understanding potyvirus evolution. J. Gen. Virol. 81:243-255.
8. Bretscher, M. T., C. L. Althaus, V. Muller, and S. Bonhoeffer. 2004. Recombination in HIV and the evolution of drug resistance: for better or for worse? Bioessays 26:180-188.
9. Bujarski, J. J., and A. M. Dzianott. 1991. Generation and analysis of non-homologous RNA-RNA recombinants in brome mosaic virus: sequence complementarities at crossover sites. J. Virol. 65:4153-4159.
10. Bujarski, J. J. 1997. Experimental systems of genetic recombination and defective RNA formation in RNA viruses: part II. Semin. Virol. 8:75-76.
11. Bunch, T., E. Rieder, and P. Mason. 1994. Sequence of the S fragment of foot-and-mouth disease virus type A12. Virus Genes 8:173-175.
12. Canto, T., S. K. Choi, and P. Palukaitis. 2001. A subpopulation of RNA 1 of cucumber mosaic virus contains 3′ termini originating from RNAs 2 or 3. J. Gen. Virol. 82:941-945.
13. Cascone, P. J., T. F. Haydar, and A. E. Simon. 1993. Sequences and structures required for recombination between virus-associated RNAs. Science 260:801-805.
14. Cheng, C. P., and P. D. Nagy. 2003. Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro. J. Virol. 77:12033-12047.
15. Dawson, W. O., D. J. Lewandowski, M. E. Hilf, P. Bubrick, A. J. Raffo, J. J. Shaw, G. L. Grantham, and P. R. Desjardins. 1989. A tobacco mosaic virus-hybrid expresses and loses an added gene. Virology 172:285-292.
16. Duarte, E. A., I. S. Novella, S. C. Weaver, E. Domingo, S. Wain-Hobson, D. K. Clarke, A. Moya, S. F. Elena, J. C. de la Torre, and J. J. Holland. 1994. RNA virus quasispecies: significance for viral disease and epidemiology. Infect. Agents Dis. 3:201-214.
17. Duggal, R., A. Cuconati, M. Gromeier, and E. Wimmer. 1997. Genetic recombination of poliovirus in a cell-free system. Proc. Natl. Acad. Sci. USA 94:13786-13791.
18. Dzianott, A., N. Rauffer-Bruyere, and J. Bujarski. 2001. Studies on functional interaction between brome mosaic virus replicase proteins during RNA recombination, using combined mutants in vivo and in vitro. Virology 289:137-149.
19. Emini, E. A., J. Leibowitz, D. C. Diamond, J. Bonin, and E. Wimmer. 1984. Recombinants of Mahoney and Sabin strain poliovirus type 1: analysis of in vitro phenotypic markers and evidence that resistance to guanidine maps in the nonstructural proteins. Virology 137:74-85.
20. French, R., and P. Ahlquist. 1987. Intercistronic as well as terminal sequences are required for efficient amplification of brome mosaic virus RNA3. J. Virol. 61:1457-1465.
21. Gmyl, A. P., and V. I. Agol. 2005. Diverse mechanisms of RNA recombination. Mol. Biol. 4:529-542.
22. Gmyl, A. P., E. V. Belousov, S. V. Maslova, E. V. Khitrina, A. B. Chetverin, and V. I. Agol. 1999. Nonreplicative RNA recombination in poliovirus. J. Virol. 73:8958-8965.
23. Guillot, S., V. Caro, N. Cuervo, E. Korotkova, M. Combiescu, A. Persu, A. Aubert-Combiescu, F. Delpeyroux, and R. Crainic. 2000. Natural genetic exchanges between vaccine and wild poliovirus strains in humans. J. Virol. 74:8434-8443.
24. Hausmann, S., D. Garcin, C. Delenda, and D. Kolakofsky. 1999. The versatility of paramyxovirus RNA polymerase stuttering. J. Virol. 73:5568-5576.
25. Huisman, M. J., B. J. C. Cornelissen, C. F. M. Groenendijk, J. F. Bol, and L. van Vloten-Doting. 1989. Alfalfa mosaic virus temperature-sensitive mutants. V. The nucleotide sequence of TBS 7 RNA 3 shows limited nucleotide changes and evidence for heterologous recombination. Virology 171:409-416.
26. Ishikawa, M., J. Diez, M. Restrepo-Hartwig, and P. Ahlquist. 1997. Yeast mutations in multiple complementation groups inhibit brome mosaic virus RNA replication and transcription and perturb regulated expression of the viral polymerase-like gene. Proc. Natl. Acad. Sci. USA 94:13810-13815.
27. Janda, M., R. French, and P. Ahlquist. 1987. High efficiency T7 polymerase synthesis of infectious RNA from cloned brome mosaic virus cDNA and effects of 5′ extensions of transcript infectivity. Virology 158:259-262.
28. Kim, M. J., and C. Kao. 2001. Factors regulating template switch in vitro by viral RNA-dependent RNA polymerases: implications for RNA-RNA recombination. Proc. Natl. Acad. Sci. USA 98:4972-4977.
29. King, A. M. 1988. Preferred sites of recombination in poliovirus RNA: an analysis of 40 intertypic crossover sequences. Nucleic Acids Res. 16:1705-1723.
30. Kirkegaard, K., and D. Baltimore. 1986. The mechanism of RNA recombination in poliovirus. Cell 47:433-443.
31. Lai, M. C. M. 1992. RNA recombination in animal and plant viruses. Microbiol. Rev. 56:61-79.
32. Li, Y., and L. A. Ball. 1993. Nonhomologous RNA recombination during negative-strand synthesis of flock house virus RNA. J. Virol. 67:3854-3860.
33. Luo, G. X., W. Luytjes, M. Enami, and P. Palese. 1991. The polyadenylation signal of influenza virus RNA involves a stretch of uridines followed by the RNA duplex of the panhandle structure. J. Virol. 65:2861-2867.
34. Moonan, F., J. Molina, and T. E. Mirkov. 2000. Sugarcane yellow leaf virus: an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors. Virology 269:156-171.
35. Nagy, P. D., and A. E. Simon. 1997. New insights into the mechanisms of RNA recombination. Virology 235:1-9.
36. Negroni, M., M. Riccheti, P. Nouvel, and H. Buc. 1995. Homologous recombination promoted by reverse transcriptase during copying of two distinct RNA templates. Proc. Natl. Acad. Sci. USA 92:6971-6975.
37. Noueiry, A. O., J. Chen, and P. Ahlquist. 2000. A mutant allele of essential, general translation initiation factor DED1 selectively inhibits translation of a viral mRNA. Proc. Natl. Acad. Sci. USA 97:12985-12990.
38. Palasingam, K., and P. N. Shaklee. 1992. Reversion of Qβ RNA phage mutants by homologous RNA recombination. J. Virol. 66:2435-2442.
39. Panavas, T., E. Serviene, J. Brasher, and P. D. Nagy. 2005. Yeast genome-wide screen reveals dissimilar sets of host genes affecting replication of RNA viruses. Proc. Natl. Acad. Sci. USA 102:7326-7333.
40. Peliska, J., and S. Benkovic. 1992. Mechanism of DNA strand transfer catalyzed by HIV-1 reverse transcriptase. Science 258:1112-1118.
41. Rabindran, S., and W. O. Dawson. 2001. Assessment of recombinants that arise from the use of a TMV-based transient expression vector. Virology 284:182-189.
42. Ranjith-Kumar, C. T., R. T. Sarisky, L. Gutshall, M. Thomson, and C. C. Kao. 2004. De novo initiation pocket mutations have multiple effects on hepatitis C virus RNA-dependent RNA polymerase activities. J. Virol. 78:12207-12217.
43. Romanova, L. I., V. M. Blinov, E. A. Tolskaya, E. G. Viktorova, M. S. Kolesnikowa, E. A. Guseva, and V. I. Agol. 1986. The primary structure of crossover regions of intertypic poliovirus recombinants: a model of recombination between RNA genomes. Virology 155:202-213.
44. Saunders, K., A. M. Q. King, D. McCahon, J. W. I. Newman, W. R. Slade, and S. Forss. 1985. Recombination and oligonucleotide analysis of guanidine-resistant foot-and-mouth disease mutants. J. Virol. 56:921-929.
45. Sivakumaran, K., Y. Bao, M. J. Roossinck, and C. C. Kao. 2000. Recognition of the core RNA promoter for minus-strand RNA synthesis by the replicases of brome mosaic virus and cucumber mosaic virus. J. Virol. 74:10323-10331.
46. Smirnyagina, E., N. S. Lin, and P. Ahlquist. 1996. The polymerase-like core of brome mosaic virus 2a protein, lacking a region interacting with viral 1a protein in vitro, maintains activity and 1a selectivity in RNA replication. J. Virol. 70:4729-4736.
47. Sullivan, M. L., and P. Ahlquist. 1999. A brome mosaic virus intergenic RNA3 replication signal functions with viral replication protein 1a to dramatically stabilize RNA in vivo. J. Virol. 73:2622-2632.
48. Sun, J. H., and C. C. Kao. 1997. RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase: transition from initiation to elongation. Virology 233:63-73.
49. Suzuki, M., T. Hibi, and C. Masuta. 2003. RNA recombination between cucumoviruses: possible role of predicted stem-loop structures and an internal subgenomic promoter-like motif. Virology 306:77-86.
50. Tolou, H. J., P. Couissinier-Paris, J. P. Durand, V. Mercier, J. J. de Pina, P. de Micco, F. Billoir, R. N. Charrel, and X. de Lamballerie. 2001. Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences. J. Gen. Virol. 82:1283-1290.
51. Tolskaya, E. A., L. A. Romanova, V. M. Blinow, E. G. Virtorova, A. N. Sinyakov, M. S. Kolesnikova, and V. I. Agol. 1987. Studies on the recombination between RNA genomes of poliovirus: the primary structure and nonrandom distribution of crossover regions in the genomes of intertypic poliovirus recombinants. Virology 161:54-61.
52. Tomita, Y., T. Mizuno, J. Díez, S. Naito, P. Ahlquist, and M. Ishikawa. 2003. Mutation of host dnaJ homolog inhibits brome mosaic virus negative-strand RNA synthesis. J. Virol. 77:2990-2997.
53. Varrelmann, M., L. Palkovics, and E. Maiss. 2000. Transgenic or plant expression vector-mediated recombination of plum pox virus. J. Virol. 74:7462-7469.
54. Weiss, B. G., and S. Schlesinger. 1991. Recombination between Sindbis virus RNAs. J. Virol. 65:4017-4025.
55. White, K. A., and T. J. Morris. 1994. Recombination between defective tombusvirus RNAs generates functional hybrid genomes. Proc. Natl. Acad. Sci. USA 91:3642-3646.
56. Wierzchoslawski, R., A. Dzianott, and J. Bujarski. 2004. Dissecting the requirement for subgenomic promoter sequences by RNA recombination of brome mosaic virus in vivo: evidence for functional separation of transcription and recombination. J. Virol. 78:8552-8564.
57. Wierechoslawski, R., A. Dzianott, S. Kunimalayan, and J. Bujarski. 2003. A transcriptionally active subgenomic promoter supports homologous crossovers in a plus-strand RNA virus. J. Virol. 77:6769-6776.
58. Wu, J. C., T. Y. Chiang, W. K. Shiue, S. Y. Wang, I. J. Sheen, Y. H. Huang, and W. J. Syu. 1999. Recombination of hepatitis D virus RNA sequences and its implications. Mol. Biol. Evol. 16:1622-1632.
59. Zhao, Y., J. Hammond, M. E. Tousignant, and R. W. Hammond. 2000. Development and evaluation of a complementation-dependent gene delivery system based on cucumber mosaic virus. Arch. Virol. 145:2285-2295.
60. Zheng, H., H. A. Lee, P. Palese, and A. Garcia-Sastre. 1999. Influenza A virus RNA polymerase has the ability to stutter at the polyadenylation site of a viral RNA template during RNA replication. J. Virol. 73:5240-5243.