Nonreplicative homologous RNA recombination: Promiscuous joining of RNA pieces?

RNA

Volumn 9, Issue 10, 2003, Pages 1221-1231

  Gmyl, Anatoly P ^a   Korshenko, Sergey A ^a   Belousov, Evgeny V ^a   Khitrina, Elena V ^a   Agol, Vadim I ^a,b  

^a CHUMAKOV INSTITUTE OF POLIOMYELITIS AND VIRAL ENCEPHALITIDES   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Evolution; Poliovirus; RNA ligation; RNA recombination

Indexed keywords

RNA; RNA POLYMERASE;

ARTICLE; GENETIC TRANSFECTION; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA RECOMBINATION; RNA SEQUENCE; RNA VIRUS;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; BASE SEQUENCE; CROSSING OVER, GENETIC; DNA PRIMERS; MOLECULAR SEQUENCE DATA; POLIOVIRUS; RECOMBINATION, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; TEMPLATES, GENETIC; TRANSCRIPTION, GENETIC; TRANSFECTION; VIRUS REPLICATION;

POLIOVIRUS; RNA VIRUSES;

EID: 0141631820     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5111803     Document Type: Article

References (66)

1. Abelson, J., Trotta, C.R., and Li, H. 1998. tRNA splicing. J. Biol. Chem. 273: 12685-12688.
2. Agol, V.I. 1997. Recombination and other genomic rearrangements in picornaviruses. Semin. Virol. 8: 1-9.
3. Agol, V.I. 2002. Picornavirus genetics: An overview. In The molecular biology of picornaviruses (eds. B.L. Semler and E. Wimmer), pp. 269-284. ASM Press, Washington, DC.
4. pol) is sufficient for template switching in vitro. J. Biol. Chem. 274: 2706-2716.
5. Avota, E., Berzins, V., Grens, E., Vishnevsky, Y., Luce, R., and Biebricher, C. 1998. The natural 6 S RNA found in Qβ-infected cells is derived from host and phage RNA. J. Mol. Biol. 276: 7-17.
6. Baroth, M., Orlich, M., Thiel, H.J., and Becher, P. 2000. Insertion of cellular NEDD8 coding sequences in a pestivirus. Virology 278: 456-466.
7. Becher, P., Orlich, M., and Thiel, H.J. 2001. RNA recombination between persisting pestivirus and a vaccine strain: Generation of cytopathogenic virus and induction of lethal disease. J. Virol. 75: 6256-6264.
8. Becher, P., Thiel, H.J., Collins, M., Brownlie, J., and Orlich, M. 2002. Cellular sequences in pestivirus genomes encoding γ-aminobutyric acid (A) receptor-associated protein and Golgi-associated ATPase enhancer of 16 kD. J. Virol. 76: 13069-13076.
9. pol): Structure, function, and mechanism. In The molecular biology of picornaviruses (eds. B.L. Semler and E. Wimmer), pp. 255-267. ASM Press, Washington, DC.
10. Charini, W.A., Todd, S., Gutman, G.A., and Semler, B.L. 1994. Transduction of a human RNA sequence by poliovirus. J. Virol. 68: 6547-6552.
11. Chetverin, A.B. 1999. The puzzle of RNA recombination. FEBS Lett. 460: 1-5.
12. Chetverin, A.B., Chetverina, H.V., Demidenko, A.A., and Ugarov, V.I. 1997. Nonhomologous RNA recombination in a cell-free system: Evidence for a transesterification mechanism guided by secondary structure. Cell 88: 503-513.
13. Chetverina, H.V., Demidenko, A.A., Ugarov, V.I., and Chetverin, A.B. 1999. Spontaneous rearrangements in RNA sequences. FEBS Lett. 450: 89-94.
14. Cooper, P.D. 1977. Genetics of picornaviruses. Comp. Virol. 9: 133-207.
15. Cruz-Reyes, J., Zhelonkina, A.G., Huang, C.E., and Sollner-Webb, B. 2002. Distinct functions of two RNA ligases in active Trypanosoma brucei RNA editing complexes. Mol. Cell Biol. 22: 4652-4660.
16. Diener, T.O. 2001. The viroid: Biological oddity or evolutionary fossil? Adv. Virus Res. 57: 137-184.
17. Doudna, J.A. and Cech, T.R. 2002. The chemical repertoire of natural ribozymes. Nature 418: 222-228.
18. Duggal, R., Cuconati, A., Gromeier, M., and Wimmer, E. 1997. Genetic recombination of poliovirus in a cell-free system. Proc. Nat. Acad. Sci. 94: 13786-13791.
19. Dzianott, A., Rauffer-Bruyere, N., and Bujarski, J.J. 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.
20. Figlerowicz, M. 2000. Role of RNA structure in nonhomologous recombination between genomic molecules of brome mosaic virus. Nucleic Acids Res. 28: 1714-1723.
21. Filipowicz, W., Konarska, M., Gross, H.J., and Shatkin, A.J. 1983. RNA 3′-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucleic Acids Res. 11: 1405-1418.
22. Genschik, P., Billy, E., Swianiewicz, M., and Filipowicz, W. 1997. The human RNA 3′-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea. EMBO J. 16: 2955-2967.
23. 54-regulated operon, J. Biol. Chem. 273: 25516-25526.
24. Gmyl, A.P., Belousov, E.V., Maslova, S.V., Khitrina, E.V., and Agol, V.I. 1999. Nonreplicative RNA recombination in poliovirus. J. Virol. 73: 8958-8965.
25. Gonzalez, T.N., Sidrauski, C., Dorfler, S., and Walter, P. 1999. Mechanism of nonspliceosomal mRNA splicing in the unfolded protein response pathway. EMBO J. 18: 3119-3132.
26. Gorbalenya, A.E. 1992. Host-related sequences in RNA viral genomes. Semin. Virol. 3: 359-371.
27. Hansen, J.L., Long, A.M., and Schultz, S.C. 1997. Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5: 1109-1122.
28. Ho, C.K. and Shuman, S. 2002. Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc. Natl. Acad. Sci. 99: 12709-12714.
29. Ikegami, M. and Fraenkel-Conrat, H. 1979. Characterization of the RNA-dependent RNA polymerase of tobacco leaves. J. Biol. Chem. 254: 149-154.
30. Izban, M.G., Parsons, M.A., and Sinden, R.R. 1998. Template end-to-end transposition by RNA polymerase II. J. Biol. Chem. 273: 27009-27016.
31. Jarvis, T.C. and Kirkegaard, K. 1991. The polymerase in its labyrinth: Mechanisms and implications of RNA recombination. Trends Genet. 7: 186-191.
32. Kandel, E.S. and Nudler, E. 2002. Template switching by RNA polymerase II in vivo. Evidence and implicaticns from a retroviral system. Mol. Cell 10: 1495-1502.
33. Khatchikian, D., Orlich, M., and Rott, R. 1989. Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus. Nature 340: 156-157.
34. Kim, M.-J. and Kao, C. 2001. Factors regulating template switch in vitro by viral RNA-dependent RNA poloymerases: Implications for RNA-RNA recombination. Proc. Nat. Acad. Sci. 98: 4972-4977.
35. Kirkegaard, K. and Baltimore, D. 1986. The mechanism of RNA recombination in poliovirus. Cell 47: 433-443.
36. Koonin, E.V. and Dolja, V.V. 1993. Evolution and taxonomy of positive-strand RNA viruses: Implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol. 28: 375-430.
37. 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.
38. Lai, M.M.C. 1992. RNA recombination in animal and plant viruses. Microbiol. Rev. 56: 61-79.
39. Lai, M.M.C and Holmes, K.V. 2001. Coronaviridae: The viruses and their replication. In Fields virology, 4th ed. (eds. D.M. Knipe and P.M. Howley), pp. 1163-1185. Lippincott, Williams and Wilkins, Philadelphia, PA.
40. Lamb, R.A. and Krug, R.M. 2001. Orthomyxoviridae: The viruses and their replication. In Fields virology, 4th ed. (eds. D.M. Knipe and P.M. Howley), pp. 1487-1531. Lippincott, Williams and Wilkins, Philadelphia, PA.
41. 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 20: 107-119.
42. Milligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15: 8783-8798.
43. Modahl, L.E., Macnaughton, T.B., Zhu, N., Johnson, D.L., and Lai, M.M.C. 2000. RNA-dependent replication and transcription of hepatitis δ virus RNA involve distinct cellular RNA polymerases. Mol. Cell. Biol. 20: 6030-6039.
44. 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. Nat. Acad. Sci. 80: 3279-3283.
45. Munishkin, A.V., Voronin, L.A., and Chetverin, A.B. 1988. An in vivo recombinant RNA capable of autocatalytic synthesis by Q βreplicase. Nature 333: 473-475.
46. Nagai, M., Sakoda, Y., Mori, M., Hayashi, M., Kida, H., and Akashi, H. 2003. Insertion of cellular sequence and RNA recombination in the structural protein coding region of cytopathogenic bovine viral diarrhoea virus. J. Gen. Virol. 84: 447-452.
47. 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. 90: 6390-6394.
48. Nagy, P.D. and Simon, A.E. 1997. New insights into the mechanisms of RNA recombination. Virology 235: 1-9.
49. Nagy, P.D., Pogany, J., and Simon, A.E. 1999. RNA elements required for RNA recombination function as replication enhancers in vitro and in vivo in a plus-strand RNA virus. EMBO J. 18:5653-5665.
50. Nishikura, K. 2001. A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst. Cell 107: 415-418.
51. Nudler, E., Avetissova, E., Markovtsov, V., and Goldfarb, A. 1996. Transcription processivity: Protein-DNA interactions holding together the elongation complex. Science 273: 211-217.
52. Pilipenko, E.V., Gmyl, A.P., Maslova, S.V., Svitkin, Y.V., Sinyakov, A.N., and Agol, V.I. 1992. A prokaryotic-like cis-element in the cap-independent internal initiation of translation on picornavirus RNA. Cell 68: 119-131.
53. Pilipenko, E.V., Gmyl, A.P., and Agol, V.I. 1995. A model for rearrangements in RNA genomes. Nucleic Acids Res. 23: 1870-1875.
54. Pleiss, J.A., Derrick, M.L., and Uhlenbeck, O.C. 1998. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. RNA 4: 1313-1317.
55. Reed, R. 2000. Mechanisms of fidelity in pre-mRNA splicing. Curr. Opin. Cell Biol. 12: 340-345.
56. Reid, C.E. and Lazinski, D.W. 2000. A host-specific function is required for ligation of a wide variety of ribozyme-processed RNAs. Proc. Natl. Acad. Sci. 97: 424-429.
57. Romani, A., Guerra, E., Trerotola, M., and Alberti, S. 2003. Detection and analysis of spliced chimeric mRNAs in sequence databanks. Nucleic Acids Res. 31: e17.
58. 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.
59. Salgia, S.R., Singh, S.K., Gurha, P., and Gupta, R. 2003. Two reactions of Haloferax volcanii RNA splicing enzymes: Joining of exons and circularization of introns. RNA 9: 319-330.
60. Schiebel, W., Haas, B., Marinkovic, S., Klanner, A., and Sänger, H.L. 1993. RNA-directed RNA polymerase from tomato leaves. II. Catalytic in vitro properties. J. Biol. Chem. 268: 11858-11867.
61. Schiebel, W., Pélissier, T., Riedel, L., Thalmeir, S., Schiebel, R., Kempe, D., Lottspeich, F., Sänger, H.L., and Wassenegger, M. 1998. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 10: 2087-2102.
62. Simpson, L., Sbicego, S., and Aphasizhev, R. 2003. Uridine insertion/ deletion RNA editing in trypanosome mitochondria: A complex business. RNA 9:265-276.
63. Singh, R. 2002. RNA-protein interactions that regulate pre-mRNA splicing. Gene Expr. 10: 79-92.
64. Tang, R.S., Barton, D.J., Flanegan, J.B., and Kirkegaard, K. 1997. Poliovirus RNA recombination in cell-free extracts. RNA 3: 624-633.
65. 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: 54-62.
66. Worobey, M. and Holmes, E.C. 1999. Evolutionary aspects of recombination in RNA viruses. J. Gen. Virol. 80: 2535-2543.