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. 1985 Jul;55(1):67–78. doi: 10.1128/jvi.55.1.67-78.1985

Evolutionary variants of Rous sarcoma virus: large deletion mutants do not result from homologous recombination.

S L Voynow, J M Coffin
PMCID: PMC254899  PMID: 2989561

Abstract

Large deletion (LD) mutants of Prague strain Rous sarcoma virus, subgroup B (PrB), derived by serial undiluted passage through chicken (C/E) cells, were isolated and characterized. Individual LD viruses were initially isolated by cloning in soft agar of infected, chemically transformed quail (QT6) cells. Two regions of the PrB genome were deleted in the formation of the LD virus. This resulted in the junction of gag sequences in p12 to env sequences in gp37, and in the loss of the src gene. DNA restriction analysis of biologically active lambda Charon 27-LD recombinant clones indicated that individual LD viruses contained similar but not identical deletion endpoints. Two LD isolates, LD25 and LD85, were further subcloned into pBR322, and the deletion junctions were examined by DNA sequencing. Although the gag-env deletion endpoints were identical in the two subclones, heterogeneity was observed across the src deletion in that both mutants analyzed had the same 5' endpoint but slightly different 3' endpoints. In all cases, only a single homologous base (always an A residue) was found at the deletion endpoint. S1 nuclease analysis of the RNA from a number of QT6-LD clones gave similar results, indicating that the LD population was composed of viruses with similar but not identical deletion endpoints. Such viruses may have been generated from errors during reverse transcription of the virion RNA with subsequent selection assuring their dominance in the population.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ahmed R., Chakraborty P. R., Fields B. N. Genetic variation during lytic reovirus infection: high-passage stocks of wild-type reovirus contain temperature-sensitive mutants. J Virol. 1980 Apr;34(1):285–287. doi: 10.1128/jvi.34.1.285-287.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bay P. H., Reichmann M. E. UV inactivation of the biological activity of defective interfering particles generated by vesicular stomatitis virus. J Virol. 1979 Dec;32(3):876–884. doi: 10.1128/jvi.32.3.876-884.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  4. Bizub D., Katz R. A., Skalka A. M. Nucleotide sequence of noncoding regions in Rous-associated virus-2: comparisons delineate conserved regions important in replication and oncogenesis. J Virol. 1984 Feb;49(2):557–565. doi: 10.1128/jvi.49.2.557-565.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Coffin J. M., Billeter M. A. A physical map of the Rous sarcoma virus genome. J Mol Biol. 1976 Jan 25;100(3):293–318. doi: 10.1016/s0022-2836(76)80065-4. [DOI] [PubMed] [Google Scholar]
  6. Coffin J. M., Tsichlis P. N., Barker C. S., Voynow S., Robinson H. L. Variation in avian retrovirus genomes. Ann N Y Acad Sci. 1980;354:410–425. doi: 10.1111/j.1749-6632.1980.tb27982.x. [DOI] [PubMed] [Google Scholar]
  7. Cullen B. R., Skalka A. M., Ju G. Endogenous avian retroviruses contain deficient promoter and leader sequences. Proc Natl Acad Sci U S A. 1983 May;80(10):2946–2950. doi: 10.1073/pnas.80.10.2946. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Czernilofsky A. P., Levinson A. D., Varmus H. E., Bishop J. M., Tischer E., Goodman H. M. Nucleotide sequence of an avian sarcoma virus oncogene (src) and proposed amino acid sequence for gene product. Nature. 1980 Sep 18;287(5779):198–203. doi: 10.1038/287198a0. [DOI] [PubMed] [Google Scholar]
  9. DeLorbe W. J., Luciw P. A., Goodman H. M., Varmus H. E., Bishop J. M. Molecular cloning and characterization of avian sarcoma virus circular DNA molecules. J Virol. 1980 Oct;36(1):50–61. doi: 10.1128/jvi.36.1.50-61.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dierks P. M., Highfield P. E., Parsons J. T. Deletion mutant of the Bratislava-77 strain of Rous sarcoma virus containing a fusion of the group-specific antigen and envelope genes. J Virol. 1979 Nov;32(2):567–582. doi: 10.1128/jvi.32.2.567-582.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dorner A. J., Stoye J. P., Coffin J. M. Molecular basis of host range variation in avian retroviruses. J Virol. 1985 Jan;53(1):32–39. doi: 10.1128/jvi.53.1.32-39.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Goff S., Traktman P., Baltimore D. Isolation and properties of Moloney murine leukemia virus mutants: use of a rapid assay for release of virion reverse transcriptase. J Virol. 1981 Apr;38(1):239–248. doi: 10.1128/jvi.38.1.239-248.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol. 1967 Jun 14;26(2):365–369. doi: 10.1016/0022-2836(67)90307-5. [DOI] [PubMed] [Google Scholar]
  14. Hughes S., Kosik E. Mutagenesis of the region between env and src of the SR-A strain of Rous sarcoma virus for the purpose of constructing helper-independent vectors. Virology. 1984 Jul 15;136(1):89–99. doi: 10.1016/0042-6822(84)90250-2. [DOI] [PubMed] [Google Scholar]
  15. Ju G., Skalka A. M. Nucleotide sequence analysis of the long terminal repeat (LTR) of avian retroviruses: structural similarities with transposable elements. Cell. 1980 Nov;22(2 Pt 2):379–386. doi: 10.1016/0092-8674(80)90348-7. [DOI] [PubMed] [Google Scholar]
  16. Katz R. A., Omer C. A., Weis J. H., Mitsialis S. A., Faras A. J., Guntaka R. V. Restriction endonuclease and nucleotide sequence analyses of molecularly cloned unintegrated avian tumor virus DNA: structure of large terminal repeats in circle junctions. J Virol. 1982 Apr;42(1):346–351. doi: 10.1128/jvi.42.1.346-351.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Majors J. E., Varmus H. E. Nucleotide sequencing of an apparent proviral copy of env mRNA defines determinants of expression of the mouse mammary tumor virus env gene. J Virol. 1983 Sep;47(3):495–504. doi: 10.1128/jvi.47.3.495-504.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  20. Meier E., Harmison G. G., Keene J. D., Schubert M. Sites of copy choice replication involved in generation of vesicular stomatitis virus defective-interfering particle RNAs. J Virol. 1984 Aug;51(2):515–521. doi: 10.1128/jvi.51.2.515-521.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mermer B., Malamy M., Coffin J. M. Rous sarcoma virus contains sequences which permit expression of the gag gene in Escherichia coli. Mol Cell Biol. 1983 Oct;3(10):1746–1758. doi: 10.1128/mcb.3.10.1746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Mitra S. W., Chow M., Champoux J., Baltimore D. Synthesis of murine leukemia virus plus strong stop DNA initiates at a unique site. J Biol Chem. 1982 Jun 10;257(11):5983–5986. [PubMed] [Google Scholar]
  23. Moscovici C., Moscovici M. G., Jimenez H., Lai M. M., Hayman M. J., Vogt P. K. Continuous tissue culture cell lines derived from chemically induced tumors of Japanese quail. Cell. 1977 May;11(1):95–103. doi: 10.1016/0092-8674(77)90320-8. [DOI] [PubMed] [Google Scholar]
  24. Nunn M., Chan S., Duesberg P. H. Complete env gene deletions of three replication-defective strains of Rous sarcoma virus and a model for the origin of their genetic structures. Virology. 1984 Apr 30;134(2):466–471. doi: 10.1016/0042-6822(84)90314-3. [DOI] [PubMed] [Google Scholar]
  25. Omer C. A., Pogue-Geile K., Guntaka R., Staskus K. A., Faras A. J. Involvement of directly repeated sequences in the generation of deletions of the avian sarcoma virus src gene. J Virol. 1983 Aug;47(2):380–382. doi: 10.1128/jvi.47.2.380-382.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Palma E. L., Huang A. Cyclic production of vesicular stomatitis virus caused by defective interfering particles. J Infect Dis. 1974 Apr;129(4):402–410. doi: 10.1093/infdis/129.4.402. [DOI] [PubMed] [Google Scholar]
  27. Panganiban A. T., Temin H. M. The terminal nucleotides of retrovirus DNA are required for integration but not virus production. Nature. 1983 Nov 10;306(5939):155–160. doi: 10.1038/306155a0. [DOI] [PubMed] [Google Scholar]
  28. Perrault J. Origin and replication of defective interfering particles. Curr Top Microbiol Immunol. 1981;93:151–207. doi: 10.1007/978-3-642-68123-3_7. [DOI] [PubMed] [Google Scholar]
  29. Reichmann M. E., Schnitzlein W. M. Defective interfering particles of rhabdoviruses. Curr Top Microbiol Immunol. 1979;86:123–168. doi: 10.1007/978-3-642-67341-2_4. [DOI] [PubMed] [Google Scholar]
  30. Rimm D. L., Horness D., Kucera J., Blattner F. R. Construction of coliphage lambda Charon vectors with BamHI cloning sites. Gene. 1980 Dec;12(3-4):301–309. doi: 10.1016/0378-1119(80)90113-4. [DOI] [PubMed] [Google Scholar]
  31. Schwartz D. E., Tizard R., Gilbert W. Nucleotide sequence of Rous sarcoma virus. Cell. 1983 Mar;32(3):853–869. doi: 10.1016/0092-8674(83)90071-5. [DOI] [PubMed] [Google Scholar]
  32. Shank P. R., Hughes S. H., Kung H. J., Majors J. E., Quintrell N., Guntaka R. V., Bishop J. M., Varmus H. E. Mapping unintegrated avian sarcoma virus DNA: termini of linear DNA bear 300 nucleotides present once or twice in two species of circular DNA. Cell. 1978 Dec;15(4):1383–1395. doi: 10.1016/0092-8674(78)90063-6. [DOI] [PubMed] [Google Scholar]
  33. Shields A., Witte W. N., Rothenberg E., Baltimore D. High frequency of aberrant expression of Moloney murine leukemia virus in clonal infections. Cell. 1978 Jul;14(3):601–609. doi: 10.1016/0092-8674(78)90245-3. [DOI] [PubMed] [Google Scholar]
  34. Shimotohno K., Temin H. M. No apparent nucleotide sequence specificity in cellular DNA juxtaposed to retrovirus proviruses. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7357–7361. doi: 10.1073/pnas.77.12.7357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Shoemaker C., Hoffman J., Goff S. P., Baltimore D. Intramolecular integration within Moloney murine leukemia virus DNA. J Virol. 1981 Oct;40(1):164–172. doi: 10.1128/jvi.40.1.164-172.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Smith J. K., Cywinski A., Taylor J. M. Initiation of plus-strand DNA synthesis during reverse transcription of an avian retrovirus genome. J Virol. 1984 Jan;49(1):200–204. doi: 10.1128/jvi.49.1.200-204.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sorge J., Hughes S. H. Polypurine tract adjacent to the U3 region of the Rous sarcoma virus genome provides a cis-acting function. J Virol. 1982 Aug;43(2):482–488. doi: 10.1128/jvi.43.2.482-488.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sorge J., Ricci W., Hughes S. H. cis-Acting RNA packaging locus in the 115-nucleotide direct repeat of Rous sarcoma virus. J Virol. 1983 Dec;48(3):667–675. doi: 10.1128/jvi.48.3.667-675.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  40. Spindler K. R., Horodyski F. M., Holland J. J. High multiplicities of infection favor rapid and random evolution of vesicular stomatitis virus. Virology. 1982 May;119(1):96–108. doi: 10.1016/0042-6822(82)90068-x. [DOI] [PubMed] [Google Scholar]
  41. Swanstrom R., Bishop J. M., Varmus H. E. Structure of a replication intermediate in the synthesis of Rous sarcoma virus DNA in vivo. J Virol. 1982 Apr;42(1):337–341. doi: 10.1128/jvi.42.1.337-341.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Tsichlis P. N., Donehower L., Hager G., Zeller N., Malavarca R., Astrin S., Skalka A. M. Sequence comparison in the crossover region of an oncogenic avian retrovirus recombinant and its nononcogenic parent: genetic regions that control growth rate and oncogenic potential. Mol Cell Biol. 1982 Nov;2(11):1331–1338. doi: 10.1128/mcb.2.11.1331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Van Beveren C., Rands E., Chattopadhyay S. K., Lowy D. R., Verma I. M. Long terminal repeat of murine retroviral DNAs: sequence analysis, host-proviral junctions, and preintegration site. J Virol. 1982 Feb;41(2):542–556. doi: 10.1128/jvi.41.2.542-556.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wahl G. M., Stern M., Stark G. R. Efficient transfer of large DNA fragments from agarose gels to diazobenzyloxymethyl-paper and rapid hybridization by using dextran sulfate. Proc Natl Acad Sci U S A. 1979 Aug;76(8):3683–3687. doi: 10.1073/pnas.76.8.3683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Wang L. H., Edelstein B., Mayer B. J. Induction of tumors and generation of recovered sarcoma viruses by, and mapping of deletions in, two molecularly cloned src deletion mutants. J Virol. 1984 Jun;50(3):904–913. doi: 10.1128/jvi.50.3.904-913.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Williams B. G., Blattner F. R. Construction and characterization of the hybrid bacteriophage lambda Charon vectors for DNA cloning. J Virol. 1979 Feb;29(2):555–575. doi: 10.1128/jvi.29.2.555-575.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Yamamoto T., Tyagi J. S., Fagan J. B., Jay G., deCrombrugghe B., Pastan I. Molecular mechanism for the capture and excision of the transforming gene of avian sarcoma virus as suggested by analysis of recombinant clones. J Virol. 1980 Aug;35(2):436–443. doi: 10.1128/jvi.35.2.436-443.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Yoshimura F. K., Yamamura J. M. Four Moloney murine leukemia virus-infected rat cell clones producing replication-defective particles: protein and nucleic acid analyses. J Virol. 1981 Jun;38(3):895–905. doi: 10.1128/jvi.38.3.895-905.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Youngner J. S., Jones E. V., Kelly M., Frielle D. W. Generation and amplification of temperature-sensitive mutants during serial undiluted passages of vesicular stomatitis virus. Virology. 1981 Jan 15;108(1):87–97. doi: 10.1016/0042-6822(81)90529-8. [DOI] [PubMed] [Google Scholar]

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