Mapping sequences active in homologous RNA recombination in brome mosaic virus: Prediction of recombination hot spots

Virology

Volumn 254, Issue 1, 1999, Pages 92-104

  Nagy, Peter D ^a,b   Ogiela, Christopher ^a   Bujarski, Jozef J ^a  

^a NORTHERN ILLINOIS UNIVERSITY   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

AU rich sequences; Bromoviruses; Mapping recombination hot spots; Misannealing; Nontemplated nucleotides; Template switching

Indexed keywords

NUCLEOTIDE; RECOMBINANT RNA; RNA DIRECTED RNA POLYMERASE;

ARTICLE; CROSSING OVER; DNA FLANKING REGION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; MOSAIC VIRUS; PLANT; PLANT VIRUS; PREDICTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE;

EID: 0033079816     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.1998.9545     Document Type: Article

References (33)

1. Ahlquist, P. A. (1992). Bromovirus RNA replication and transcription. Curr. Opin. Genet. Dev. 2, 71-76.
2. Ahlquist P. A., Dasgupta, R., and Kaesberg, P. (1984). Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication. J. Mol. Biol. 172, 369-383.
3. Allison, R. F., Thompson, G., and Ahlquist, P. (1990). Regeneration of a functional RNA virus genome by recombination between deletion mutants and requirement for cowpea chlorotic mottle virus 3a and coat genes for systemic infection. Proc. Natl. Acad. Sci. USA 87, 1820-1824.
4. Bujarski, J. J., and Kaesberg, P. (1986). Genetic recombination between RNA components of a multipartite plant virus. Nature 321, 528-531.
5. Bujarski, J. J., and Nagy, P. D. (1994). Genetic RNA-RNA recombination in positive-stranded RNA viruses of plants. In "Homologous Recombination in Plants" (J. Paszkowski, Ed.), pp. 1-24. Kluwer Academic Publisher, Dordrecht, The Netherlands.
6. Bujarski, J. J., and Nagy, P. D. (1996). Different mechanisms of homologous and nonhomologous recombination in brome mosaic virus: Role of RNA sequences and replicase proteins. Semin. Virol. 7, 363-372.
7. Carpenter, C. D., and Simon, A. E. (1994). Recombination between plus and minus strands of turnip crinkle virus. Virology 201, 419-423.
8. Dzianott, A., Flasinski, S., Pratt, S., and Bujarski, J. (1995). Foreign complementary sequences facilitate genetic recombination in brome mosaic virus. Virology 208, 370-375.
9. Figlerowicz, M., Nagy, P. D., and Bujarski, J. J. (1997). A mutation in the putative RNA polymerase gene inhibits nonhomologous, but not homologous, genetic recombination in an RNA virus. Proc. Natl. Acad. Sci. USA 94, 2073-2078.
10. Havelda, Z., Dalmay, T., and Burgyan, J. (1997). Secondary structure-dependent evolution of cymbidium ringspot virus defective interfering RNA. J. Gen. Virol. 78, 1227-1234.
11. Janda, M., French, R., and Ahlquist, P. A. (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.
12. Jarvis, T. C., and Kirkegaard, K. (1992). Poliovirus RNA recombination: Mechanistic studies in the absence of selection. EMBO J. 11, 3135-3145.
13. King, A. M. Q. (1988). Genetic recombination in positive strand RNA viruses. In "RNA Genetics" (E. Domingo, J. J. Holland, and P. Ahlquist, Eds.), vol. II, pp. 149-185. CRC Press, Boca Raton, FL.
14. Kirkegaard, K., and Baltimore, D. (1986). The mechanism of RNA recombination in Poliovirus. Cell 47, 433-443.
15. Koetzner, C. A., Parker, M. M., Ricard, C. S., Sturman, L. S., and Masters, P. S. (1992). Repair and mutagenesis of the genome of a deletion mutant of the coronavirus mouse hepatitis virus by targeted RNA recombination. J. Virol. 66, 1841-1848.
16. Lai, M. C. M. (1992). RNA recombination in animal and plant viruses. Microbiol. Rev. 56, 61-79.
17. Makino, S., Fleming, J. O., Keck, J. G., Stohlman, S. A., and Lai, M. M. C. (1987). RNA recombination of coronaviruses: Localization of neutralizing epitopes and neuropathogenic determinants on the carboxyl terminus of peplomers. Proc. Natl. Acad. Sci. USA 84, 6567-6571.
18. Nagy, P. D., and Bujarski, J. J. (1992). Genetic recombination in brome mosaic virus: Effect of sequence and replication of RNA on accumulation of recombinants. J. Virol. 66, 6824-6828.
19. Nagy, P. D., and Bujarski, J. J. (1993). Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences. Proc. Natl. Acad. Sci. USA 90, 6390-6394.
20. Nagy, P. D., and Bujarski, J. J. (1995). Efficient system of homologous RNA recombination in brome mosaic virus: Sequence and structure requirements and accuracy of crossovers. J. Virol. 69, 131-140.
21. Nagy, P. D., and Bujarski, J. J. (1996). Homologous RNA recombination in brome mosaic virus: Au-rich sequences decrease the accuracy of crossovers. J. Virol. 70, 415-426.
22. Nagy, P. D., and Bujarski, J. J. (1997). Engineering of homologous recombination hotspots with AU-rich sequences in brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers. J. Virol. 71, 3799-3810.
23. Nagy, P. D., and Bujarski, J. J. (1998). Silencing homologous recombination hot spots with GC-rich sequences in brome mosaic virus. J. Virol. 72, 1122-1130.
24. Nagy, P. D., Dzianott, A., Ahlquist, P., and Bujarski, J. J. (1995). Mutations in the helicase-like domain of protein 1a alter the sites of RNA-RNA recombination in brome mosaic virus. J. Virol. 69, 2547-2556.
25. Nagy, P. D., and Simon, A. E. (1997). New insights into the mechanisms of RNA recombination. Virology 235, 1-9.
26. Palasingam, K., and Shaklee, P. N. (1992). Reversion of qb RNA phage mutants by homologous RNA recombination. J. Virol. 66, 2435-2442.
27. Pathak, V. K., and Hu, W-S. (1997). "Might as well jump!" template switching by retroviral reverse transcriptase, defective genome formation, and recombination. Semin. Virol. 8, 141-150.
28. Pogany, J., Romero, J., Huang, Q., Sgro, J.-Y., Shang, H., and Bujarski, J. J. (1995). De novo generation of defective interfering-like RNAs in broad bean mottle bromovirus. Virology 212, 574-586.
29. Raju, R., Subramaniam, S. V., and Hajjou, M. (1995). Genesis of sindbis virus by in vivo recombination of nonreplicative RNA precursors. J. Virol. 69, 7391-7401.
30. Rao, A. L. N., and Hall, T. C. (1993). Recombination and polymerase error facilitate restoration of infectivity in brome mosaic virus. J. Virol. 67, 969-979.
31. Romanova, L. I., Blinov, V. M., Tolskaya, E. A., Viktorova, E. G., KolesniKova, M. S., Guseva, E. A., and Agol, V. I. (1986). The primary structure of crossover regions of intertypic poliovirus recombinants: A model of recombination between RNA genomes. Virology 155, 202-213.
32. Van Der Most, R. G., Heijnen, L. Spaan, W. J. M., and DeGroot, R. J. (1992). Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs. Nucleic Acids Res. 20, 3375-3381.
33. White, K. A., and Morris, T. J. (1995). RNA determinants of junction site selection in RNA virus defective interfering RNAs. RNA 1, 1029-1040.