Homologous RNA recombination in brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers

Journal of Virology

Volumn 70, Issue 1, 1996, Pages 415-426

  Nagy, Peter D ^a   Bujarski, Jozef J ^a  

^a NORTHERN ILLINOIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RECOMBINANT RNA;

ARTICLE; GENE DELETION; MOLECULAR CLONING; MOSAIC VIRUS; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS GENE;

BASE SEQUENCE; BINDING SITES; BROMOVIRUS; CROSSING OVER (GENETICS); MOLECULAR SEQUENCE DATA; POLY A-U; RECOMBINATION, GENETIC; RNA; RNA, VIRAL; SEQUENCE DELETION; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, NON-P.H.S.; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0029656131     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.70.1.415-426.1996     Document Type: Article

References (57)

1. Ahlquist, P. 1992. Bromovirus RNA replication and transcription. Curr. Opin. Genet. Dev. 2:71-76.
2. Ahlquist, P., R. Dasgupta, and P. Kaesberg. 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., M. Janda, and P. Ahlquist. 1989. Sequence of cowpea chlorotic mottle virus RNAs 2 and 3 and evidence of a recombination event during bromovirus evolution Virology 172:321-330
4. Allison, R. F., G. Thompson, and P. Ahlquist. 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
5. Beck, D. L., and W. O. Dawson. 1990. Deletion of repeated sequences from tobacco mosaic virus mutants with two coal protein genes. Virology 177:462-469
6. Bergmann, M., A. Gareia-Sastre, and P. Palese. 1992. Transfection mediated recombination of influenza A virus. J Virol 66:7576-7580.
7. Bertholet, C., E. van Meir, B. ten Heggeler-Bordier, and R. Wittek. 1987. Vaccinia virus produces late mRNAs by discontinuous synthesis Cell 50:153-162.
8. Biebricher, C. K., and R. Luce. 1992. In vitro recombination and terminal elongation of RNA by Oβ replicase EMBO J 11:5129-5135.
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., and P. Kaesberg. 1986. Genetic recombination between RNA components of a multipartite plant virus Nature (London) 321:528-531.
11. Bujarski, J. J., and P. D. Nagy. 1994. Genetic RNA-RNA recombination in positive-stranded RNA viruses of plants, p. 1-24. In J. Paszkowski (ed.), Homologous recombination in plants. Kluwer Academic Publisher, Dordrecht, The Netherlands.
12. Bujarski, J. J., P. D. Nagy, and S. Flasinski. 1994. Molecular studies of genetic RNA-RNA recombination in brome mosaic virus. Adv. Virus Res. 43:275-302.
13. Cascone, P. J., C. D. Carpenter, X. H. Li, and A. E. Simon. 1990. Recombination between satellite RNAs of turnip crinkle virus. EMBO J. 9:1709-1715.
14. 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
15. Dolja, V. V., and J. C. Carrington. 1992. Evolution of positive strand RNA viruses. Semin. Virol 3:315-326.
16. Goldbach, R., O. Le Gall, and J. Wellink. 1991. Alpha-like viruses in plants. Semin. Virol. 2:19-25.
17. Greene, A. E., and R. F. Allison. 1994. Recombination between viral RNA and transgenic plant transcripts. Science 263:1423-1425.
18. Ishikawa, M., P. Kroner, P. Ahlquist, and T. Meshi. 1991. Biological activities of hybrid RNAs generated by 3′-end exchanges between tobacco mosaic and brome mosaic viruses. J. Virol 65:3451-3459.
19. Jacobsen, A. B., L. Good, J. Simonetti, and M. Zuker. 1984. Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res. 12:45-52.
20. Jacques, J. P., S. Hausmann, and D. Kolakofsky. 1994. Paramyxovirus mRNA editing leads to G deletions as well as insertions. EMBO J. 13:5496-5503.
21. 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.
22. Jarvis, T. C., and K. Kirkegaard. 1991. The polymerase in its labyrinth: mechanisms and implications of RNA recombination Trends Genet. 7:186-191.
23. Jarvis, T. C., and K. Kirkegaard. 1992. Poliovirus RNA recombination: mechanistic studies in the absence of selection EMBO J. 11:3135-3145.
24. King, A. M. Q. 1988. Genetic recombination in positive strand RNA viruses, p. 149-185. In E. Domingo, J J. Holland, and P. Ahlquist (ed), RNA genetics, vol. 2 CRC Press, Boca Raton, Fla.
25. Kirkegaard, K., and D. Baltimore. 1986. The mechanism of RNA recombination in poliovirus. Cell 47:433-443.
26. Kroner, P., D. Richards, P. Traynor, and P. Ahlquist. 1989. Defined mutations in a small region of the brome mosaic virus 2a gene cause diverse temperature-sensitive RNA replication phenotypes. J. Virol. 63:5302-5309.
27. Kuge, S., I. Saito, and A. Nomoto. 1986. Primary structure of poliovirus defective-interfering particule genomes and possible generation mechanisms of the particules. J. Mol. Biol 192:473-487
28. Lahser, F. C., L. E. Marsh, and T. C. Hall. 1993. Contributions of the brome mosaic virus RNA-3 3′-nontranslated region to replication and translation. J. Virol. 67:3295-3303
29. Lai, M. M. C. 1992. RNA recombination in animal and plant viruses. Microbiol. Rev. 56:61-79.
30. Lane, L. C. 1977. Brome mosaic virus CM1/AAB descriptions of plant viruses no. 180 Commonwealth Agricultural Bureaux, Farnham Royal, Slough, England.
31. Li, Y., and L. A. Ball. 1993. Nonhomologous RNA recombination during negative-strand synthesis of flock house virus RNA J. Virol. 67:3854-3860.
32. Luo, G., 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.
33. Makino, S., J. G. Keck, S. A. Stohlman, and M. M. C. Lai. 1986. High-frequency RNA recombination of murine coronaviruses. J. Virol. 57:729-737.
34. Marsh, L. E., G. P. Pogue, C. C. Huntley, and T. C. Hall. 1991. Insight to replication strategies and evolution of (+) strand RNA viruses provided by brome mosaic virus. Oxf Surv. Plant Mol. Cell Biol. 7:297-334.
35. Nagy, P. D., and J. J. Bujarski. 1992. Genetic recombination in brome mosaic virus effect of sequence and replication of RNA on accumulation of recombinants J Virol. 66:6824-6828.
36. Nagv, P. D., and J. J. Bujarski. 1993. Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences. Proc Natl. Acad Sci. USA 90:6390-6394.
37. Nagv, P. D., and J. J. Bujarski. 1995. Efficient system of homologous RNA recombination in brome mosaic virus: sequence and structure requirements and accuracy of crossovers. J Virol. 69:131-140.
38. Nagy, P. D., A. Dzianott, P. Ahlquist, and J. J. Bujarski. 1995. Mutations in the helicase-like domain of protein la alter the sites of RNA-RNA recombination in brome mosaic virus. J. Virol. 69:2547-2556.
39. Onodera, S., X. Qiao, P. Gottlieb, J. Strassman, M. Frilander, and L. Mindich. 1993. RNA structure and heterologous recombination in the double-stranded RNA bacteriophage 46. J. Virol 67:4914-4922.
40. Palasingam, K., and P. N. Shaklee. 1992. Reversion of Qβ RNA phage mutants by homologous RNA recombination. J. Virol. 66:2435-2442
41. Raffo, A. J., and W. O. Dawson. 1991. Construction of tobacco mosaic virus subgenomic replicons that are replicated and spread systemically in tobacco plants. Virology 184:277-289.
42. Rao, A. L. N., and T. C. Hall. 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. 64:2437-2441.
43. Rao, A. L. N., and T. C. Hall. 1993. Recombination and polymerase error facilitate restoration of infectivity in brome mosaic virus. J. Virol. 67:969-979.
44. Rao, A. L. N., B. P. Sullivan, and T. C. Hall. 1990. Use of Chenopodium hybridum facilitates isolation of brome mosaic virus RNA recombinants. J Gen. Virol. 71:1403-1407.
45. Romanova, L. I., V. M. Blinov, E. A. Tolskaya, E. G. Viktorova, M. S. Kolesnikova, 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
46. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning, a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
47. Strauss, J. H., and E. G. Strauss. 1988. Evolution of RNA viruses. Annu. Rev. Microbiol. 42:657-683.
48. Thomas, S. M., R. A. Lamb, and R. G. Paterson. 1988 Two mRNAs that differ by two nontemptated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5. Cell 54:891-902
49. Tolskaya, E. A., L. I. Romanova, V. M. Blinov, E. G. Viktorova, 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.
50. Van der Kuyl, A. C., L. Necleman, and J. F. Bol. 1991. Complementation and recombination between alfalfa mosaic virus RNA3 mutants in tobacco plants Virology 183:731-738.
51. van der Most, R. G., R. J. de Groot, and W. J. M. Spaan. 1994. Subgenomic RNA synthesis directed by a synthetic defective interfering RNA of mouse hepatitis virus: a study of coronavirus transcription initiation. J. Virol 68:3656-3666
52. Van der Most, R. G., L. Heijnen, W. J. M. Spaan, and R. J. de Groot. 1992 Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicaling RNAs. Nucleic Acids Res. 20:3375-3381.
53. Weiss, B. G., and S. Schlesinger. 1991. Recombination between Sindbis virus RNAs. J Virol. 65:4017-4025.
54. White, K. A., and T. J. Morris. 1994. Nonhomologous RNA recombination in tombusviruses: generation and evolution of defective interfering RNAs by stepwise deletions J. Virol. 68:14-24.
55. White, K. A., and T. J. Morris. 1994. Recombination between defective tonibusvirub RNAs generates functional hybrid genomes. Proc. Natl. Acad. Sci. USA 91:3642-3646.
56. Zhang, X., and M. M. C. Lai. 1994 Unusual heterogeneity of leader-mRNA fusion in a murine coronavirus. implications for the mechanism of RNA transcription and recombination. J. Virol. 68:6626-6633.
57. Zimmern, D. 1988. Evolution of RNA viruses, p. 211-240. In E. Domingo, J. J. Holland, and P Ahlquist (ed), RNA genetics, vol. 2. CRC Press, Boca Raton. Fla.