Different Mechanisms of Homologous and Nonhomologous Recombination in Brome Mosaic Virus, a Model Plant RNA Virus

  • Jozef J. Bujarski
Conference paper


Brome mosaic bromovirus, a tripartite, positive-stranded RNA virus of plants, can generate both homologous and nonhomologous intersegment RNA recombinants in vivo. The use of specially designed BMV RNA recombination vectors has demonstrated that recombination signals in the RNAs were different for these two recombination types. Specifically, nonhomologous recombination requires the formation of local double-stranded regions between the recombining RNAs while homologous recombination is facilitated by AU-rich sequences in conjunction with upstream GC-rich regions, common in the RNA substrates. These features most likely reflect different mechanisms involved in homologous and nonhomologous crossovers for this RNA virus.

To study if BMV replicase is involved in RNA recombination, viable mutants in both la and 2a replicase polypeptides were tested. Specifically, mutations within the helicase domain of la affected the location of crossover sites in nonhomologous recombination. This demonstrates that la protein is involved in nonhomologous recombination, most likely in unwinding double-stranded regions between the recombining RNAs. Mutations in the core domain of 2a, the RNA polymerase component, have reduced nonhomologous recombination below the level of detection, without affecting noticeably homologous recombination. All these observations confirm the existence of differences in the molecular mechanisms of both recombination types.


Homologous Recombination Helicase Domain Junction Site Brome Mosaic Virus Recombination Type 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Ahlquist P (1992) Bromovirus RNA replication and transcription. Curr Opin Genet Dev 2:71–76PubMedCrossRefGoogle Scholar
  2. Allison RF, Thompson G, 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 Nat Acad Sci USA 87:1820–1824PubMedCrossRefGoogle Scholar
  3. Bujarski JJ, Dzianott AM (1991) Generation and analysis of nonhomologous RNA-RNA recombinants in brome mosaic virus: Sequence complementarities at crossover sites. J Virol 65:4153–4159PubMedGoogle Scholar
  4. Bujarski JJ, Kaesberg P (1986) Genetic recombination between RNA components of a multipartite plant virus. Nature 321:528–531PubMedCrossRefGoogle Scholar
  5. Bujarski JJ, Nagy PD (1994) Genetic RNA-RNA recombination in positive-stranded RNA viruses of plants. In: Paszkowski J (ed) Homologous recombination in plants, p. 1–24. Kluwer Academic Publisher, Dordrecht, The NetherlandsCrossRefGoogle Scholar
  6. Bujarski JJ, Nagy PD, Flasinski S (1994) Molecular studies of genetic RNA-RNA recombination in brome mosaic virus. Adv Virus Res 43:275–302PubMedCrossRefGoogle Scholar
  7. Chamberlin MJ (1995) New models for the mechanism of transcription elongation and its regulation. Harvey Lect 88:1–21Google Scholar
  8. Cooper P. (1977) Genetics of picornaviruses. In: Fraenkel-Conradt H, Wagner R (ed) Comprehensive Virology Vol. 9, pp. 133–207. Plenum Press, New YorkGoogle Scholar
  9. Figlerowicz M, Nagy PD, Bujarski JJ (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 94:2073–2078PubMedCrossRefGoogle Scholar
  10. Hirst GK (1962) Genetic recombination with Newcastle disease virus, polioviruses, and influenza virus. Cold. Spring Harbor Quant. Biol. 27:303–309CrossRefGoogle Scholar
  11. Ishikawa M, Kroner P, Ahlquist P, Meshi T (1991) Biological activities of hybrid RNAs generated by 3′-end exchanges between tobacco mosaic and brome mosaic viruses. J Virol 65:3451–3459PubMedGoogle Scholar
  12. Kao CC, Ahlquist P (1992) Identification of the domains required for direct interaction of the helicase-like and polymerase-like RNA replication proteins of brome mosaic virus. J Virol 66:7293–7302PubMedGoogle Scholar
  13. Lai MMC, Baric RS, Makino S, Keck JG, Egbert J, Leibowitz JL, Stohlman SA (1985) Recombination between nonsegmented RNA genomes of murine coronaviruses. J Virol 56:449–456PubMedGoogle Scholar
  14. Ledinko N (1963) Genetic recombination with poliovirus type 1: studies of crosses between a normal horse serum-resistant mutants of the same strain. Virology 20:107–119PubMedCrossRefGoogle Scholar
  15. Nagy PD, Bujarski JJ (1992) Genetic recombination in brome mosaic virus: effect of sequence and replication of RNA on accumulation of recombinants. J Virol 66:6824–6828PubMedGoogle Scholar
  16. Nagy PD, Bujarski JJ (1993) Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences. Proc Natl Acad Sci USA 90:6390–6394PubMedCrossRefGoogle Scholar
  17. Nagy PD, Bujarski JJ (1995) Efficient system of homologous RNA recombination in brome mosaic virus: Sequence and structure requirements and accuracy of crossovers. J Virol 69:131–140PubMedGoogle Scholar
  18. Nagy PD, Bujarski JJ (1996) Homologous RNA recombination in brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers. J Virol 70:415–426PubMedGoogle Scholar
  19. Nagy PD, Bujarski JJ (1997) Engineering of homologous recombination hotspots with AU-rich sequences in brome mosaic virus. J. Virol 71:1294–1306Google Scholar
  20. Nagy PD, Dzianott A, Ahiquist P, Bujarski JJ (1995) Mutations in the helicase-like domain of protein la alter the sites of RNA-RNA recombination in brome mosaic virus. J Virol 69:2547–2556PubMedGoogle Scholar
  21. Rao ALN, Hall TC (1990) Requirement for a viral trans-acting factor encoded by brome mosaic virus RNA-2 provides strong selection in vivo for functional recombinants. J Virol 64:2437–2441PubMedGoogle Scholar
  22. Rao ALN, Sullivan BP, Hall TC (1990) Use of Chenopodium hybridum facilitates isolation of brome mosaic virus RNA recombinants. J Gen Virol 71:1403–1407PubMedCrossRefGoogle Scholar
  23. Simon AE, Bujarski JJ (1994) RNA-RNA recombination and evolution in virus infected plants. Annu Rev Phythopathol 32:337–362CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1997

Authors and Affiliations

  • Jozef J. Bujarski
    • 1
  1. 1.Plant Molecular Biology Center and the Department of Biological SciencesNorthern Illinois UniversityDeKalbUSA

Personalised recommendations