Nonhomologous RNA recombination in a cell-free system: Evidence for a transesterification mechanism guided by secondary structure

Cell

Volumn 88, Issue 4, 1997, Pages 503-513

  Chetverin, Alexander B ^a   Chetverina, Helena V ^a   Demidenko, Alexander A ^a   Ugarov, Victor I ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHATE; Q BETA REPLICASE; RECOMBINANT RNA; RIBONUCLEOSIDE DERIVATIVE;

ARTICLE; CELL FREE SYSTEM; GENETIC RECOMBINATION; PRIORITY JOURNAL; RNA REPLICATION; RNA SPLICING; RNA STRUCTURE;

EID: 0030975364     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81890-5     Document Type: Article

References (38)

1. Berestowskaya, N.H., Vasiliev, V.D., Volkov, A.A., and Chetverin, A.B. (1988). Electron microscopy study of Qβ replicase. FEBS Lett. 228, 263-267.
2. Biebricher, C.K., Diekmann, S., and Luce, R. (1982). Structural analysis of self-replicating RNA synthesized by Qβ replicase. J. Mol. Biol. 154, 629-648.
3. Biebricher, C.K., and Luce, R. (1992). In vitro recombination and terminal elongation of RNA by Qβ replicase. EMBO J. 11, 5129-5135.
4. Blumenthal, T. (1979). Qβ RNA replicase and protein synthesis elongation factors EF-Tu and EF-Ts. Methods Enzymol. 60, 628-638.
5. Carpenter, C.D., Oh, J.-W., Zhang, C., and Simon, A.E. (1995). Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination. J. Mol. Biol. 245, 608-622.
6. Cech, T.R., and Bass, B.L. (1986). Biological catalysis by RNA. Ann. Rev. Biochem. 55, 599-629.
7. Chetverin, A.B., Chetverina, H.V.,and Munishkin, A.V. (1991). On the nature of spontaneous RNA synthesis by Qβ replicase. J. Mol. Biol. 222, 3-9.
8. Chetverin, A.B., Voronin, L.A., Munishkin, A.V., Bondareva, L.A., Chetverina, H.V., and Ugarov, V.I. (1992). Recombination in replicating RNAs. In Frontiers in Bioprocessing II, P. Todd, S.K. Sikdar and M. Bier, eds. (Washington, DC: American Chemical Society), pp. 44-49.
9. Chetverin, A.B., and Spirin, A.S. (1995). Replicable RNA vectors: prospects for cell-free gene amplification, expression and cloning. In Progress in Nucleic Acid Research and Molecular Biology, W.E. Cohn and K. Moldave, eds. (San Diego, California: Academic Press), vol. 51, pp. 225-270.
10. Chetverina, H.V., and Chetverin, A.B. (1993). Cloning of RNA molecules in vitro. Nucleic Acids Res. 21, 2349-2353.
11. Cooper, P.D., Steiner-Pryor, S., Scotti, P.D., and Delong, D. (1974). On the nature of poliovirus genetic recombinants. J. Gen. Virol. 23, 41-49.
12. Dzianott, A., Flasinski, S., and Bujarski, J.J. (1995). Foreign complementary sequences facilitate genetic RNA recombination in brome mosaic virus. Virology 208, 370-375.
13. Gilbert, W. (1986). The RNA world. Nature 379, 618.
14. Hajjou, M., Hill, K.,Subramaniam, S.V., Hu, J.Y., and Raju, R. (1996). Nonhomologous RNA-RNA recombination events at the 3′ nontranslated region of the Sindbis virus genome: hot spots and utilization of nonviral sequences. J. Virol. 70, 5153-5164.
15. Hirst, G.K. (1962). Genetic recombination with Newcastle disease virus, poliovirus and influenza virus. Cold Spring Harbor Symp. Quant. Biol. 27, 303-309.
16. Igloi, G.L. (1983). A silver stain for the detection of nanogram amounts of tRNA following two-dimensional electrophoresis. Anal. Biochem. 134, 184-188.
17. Jarvis, T.C., and Kirkegaard, K. (1992). Poliovirus RNA recombination: mechanistic studies in the absence of selection. EMBO J. 11, 3135-3145.
18. Kirkegaard, K., and Baltimore, D. (1986). The mechanism of RNA recombination in poliovirus. Cell 47, 433-443.
19. Kuge, S., Saito, I., and Nomoto, A. (1986). Primary structure of poliovirus defective-interfering particle genomes and possible generation mechanisms of the particles. J. Mol. Biol. 192, 473-487.
20. Lai, M.M.C. (1992). RNA recombination in animal and plant viruses. Microbiol. Rev. 56, 61-79.
21. Ledinko, N. (1963). Genetic recombination with poliovirus type 1: studies of crosses between a normal horse serum-resistant mutant and several guanidine-resistant mutants of the same strain. Virology 180, 107-119.
22. Milligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. (1987). Oligonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798.
23. Milligan, J.F., and Uhlenbeck, O.C. (1989). Determination of RNA-protein contacts using thiophosphate substitutions. Biochemistry 28, 2849-2855.
24. Monroe, S.S., and Schlesinger, S. (1983). RNAs from two independently isolated defective interfering particles of Sindbis virus contain a cellular tRNA sequence at their 5'-ends. Proc. Natl. Acad. Sci. USA 80, 3279-3283.
25. Moody, M.D., Burg, J.L., DiFrancesco, R., Lovern, D., Stanik, W., Lin-Goerke, J., Mahdavi, K., Wu, Y., and Farrel, M.P. (1994). Evolution of host cell RNA into efficient template RNA by Qβ replicase: the origin of RNA in untemplated reactions. Biochemistry 33, 13836-13847.
26. Morozov, I.Y., Ugarov, V.I., Chetverin, A.B., and Spirin, A.S. (1993). Synergism in replication and translation of messenger RNA in a cell-free system. Proc. Natl. Acad. Sci. USA 90, 9325-9329.
27. Munishkin, A.V., Voronin, L.A., and Chetverin, A.B. (1988). An in vivo recombinant RNA capable of autocatalytic synthesis by Qβ replicase. Nature 333, 473-475.
28. Munishkin, A.V., Voronin, L.A., Ugarov, V.I., Bondareva, L.A., Chetverina, H.V., and Chetverin, A.B. (1991). Efficient templates for Qβ replicase are formed by recombination from heterologous sequences. J. Mol. Biol. 221, 463-472.
29. 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.
30. Negroni, M., Riccheti, M., Nouvel, P., and Buc, H. (1995). Homologous recombination by reverse transcriptase during copying of two distinct RNA templates. Proc. Natl. Acad. Sci. USA 92, 6971-6975.
31. Noren, C.J., Anthony-Cahill, S.J., Suich, D.J., Noren, K.A., Griffith, M.C., and Schultz, P.G. (1990). In vitro suppression of an amber mutation by a chemically aminoacylated transfer RNA prepared by runoff transcription. Nucleic Acids Res. 18, 83-88.
32. Palasingam, K., and Shaklee, P.N. (1992). Reversion of Qβ phage mutants by homologous RNA recombination. J. Virol. 66, 2435-2442.
33. 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.
34. Steinschneider, A., and Fraenkel-Conrat, H. (1966a). Studies of nucleotide sequences in tobacco mosaic virus ribonucleic acid. III. Periodate oxidation and semicarbazone formation. Biochemistry 5, 2729-2734.
35. Steinschneider, A., and Fraenkel-Conrat, H. (1966b). Studies of nucleotide sequences in tobacco mosaic virus ribonucleic acid. IV. Use of aniline in stepwise degradation. Biochemistry 5, 2735-2743.
36. Tolskaya, E.A., Romanova, L.I., Blinov, V.M., Viktorova, E.G., Sinyakov, A.N., Kolesnikova, M.S., and Agol, V.I. (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.
37. Weissmann, C. (1974). The making of a phage. FEBS Lett. 40, S10-S18.
38. Zuker, M., and Stiegler, P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148.