Petunia vein-clearing virus: A plant pararetrovirus with the core sequences for an integrase function

Virology

Volumn 236, Issue 1, 1997, Pages 137-146

  Richert Poggeler K R ^a   Shepherd, R J ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; CAULIFLOWER MOSAIC VIRUS; CELL INCLUSION; CONTROLLED STUDY; NONHUMAN; PHYLOGENY; PLANT; PLANT VIRUS; PRIORITY JOURNAL; RETROPOSON; VIRUS CORE;

BRASSICA OLERACEA VAR. BOTRYTIS; CAULIFLOWER MOSAIC VIRUS; MIRIDAE; PETUNIA; PETUNIA VEIN CLEARING VIRUS;

EID: 0031572266     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.1997.8712     Document Type: Article

References (60)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Atwood, A., Lin, J.-H., and Levin, H. L. (1996). The retrotransposon Tf1 assembles virus-like particles that contain excess gag relative to integrase because of a regulated degradation process. Mol. Cell. Biol. 16, 338-346.
3. Boeke, J. D., and Corces, V. G. (1989). Transcription and reverse transcription of retrotransposons. Annu. Rev. Microbiol. 43, 403-434.
4. Bouchez, D., Tokuhisa, J. G., Llewellyn, D. J., Dennis, E. S., and Ellis, J. G. (1989). The ocs-element is a component of the promoters of several T-DNA and plant viral genes. EMBO J. 8, 4197-4204.
5. Bouhida, M., Lockhart, B. E. L., and Olszewski, N. E. (1993). An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice. J. Gen. Virol. 74, 15-22.
6. Britten, R. J. (1995). Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 92, 599-601.
7. Calvert, L. A., Ospina, M. D., and Shepherd, R. J. (1995). Characterization of cassava vein mosaic virus: A distinct plant pararetrovirus. J. Gen. Virol. 76, 1271-1276.
8. Covey, S. N. (1985). Organization and expression of the cauliflower mosaic virus genome. In "Molecular Plant Virology," Vol. 2, "Replication and Gene Expression" (J. W. Davies, Ed.), pp. 121-159. CRC Press, Boca Raton, FL.
9. Covey, S. N. (1986). Amino acid sequence homology in gag region of reverse transcribing elements and the coat protein gene of cauliflower mosaic virus. Nucleic Acids Res. 14, 623-633.
10. Dayhoff, M. O. (1979). "Atlas of Protein Sequence and Structure," Vol. 5, Suppl. 3, 1978. Natl. Biomed. Res. Found., Washington, DC.
11. Devereux, J., Haeberli, P., and Smithies, O. (1984). A comprehensive set for sequence analysis for the VAX. Nucleic Acids Res. 12, 387-395.
12. Doolittle, R. F., and Feng, D. F. (1992). Tracing the origin of retroviruses. Curr. Top. Microbiol. Immunol. 176, 195-211.
13. Drelich, M., Wilhelm, R., and Mous, J. (1992). Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 IN protein in vitro. Virology 188, 459-468.
14. Ducasse, D. A. (1991). Gene I of peanut chlorotic streak virus (caulimovirus group) - Is it involved in virus movement? pp. 33-41. Univ. of Kentucky, Lexington. [Ph.D. Thesis]
15. Eickbush, T. H. (1994). Origin and evolutionary relationships of retroelements. In "The Evolutionary Biology of Viruses" (S. S. Morse, Ed.), pp. 121-157. Raven Press, New York.
16. Engelman, A., and Craigie, R. (1992). Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol. 66, 6361-6369.
17. Farman, M. L., Tosa, Y., Nitta, N., and Leong, S. A. (1996). MAGGY, a retrotransposon in the genome of the rice blast fungus Magnaporthe grisea. Mol. Gen. Genet. 251, 665-674.
18. Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package), Version 3.5c. Univ. of Washington, Seattle.
19. Friesen, P. D., and Nissen, M. S. (1990). Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome. Mol. Cell. Biol. 10, 3067-3077.
20. Gardner, R. C., and Shepherd, R. J. (1980). A procedure for rapid isolation and analysis of cauliflower mosaic virus DNA. Virology 106, 159-161.
21. Hagen, L.S., Jacquemond, M., Lepingle, A., Lot, H., and Tepfer, M. (1993). Nucleotide sequence and genomic organization of cacao swollen shoot virus. Virology 196, 619-628.
22. Hansen, M., Albers, M., Backes, U., Coblenz, A., Leuther, H., Neu, R., Schreer, A., Schaefer, B., Zimmermann, M., and Wolf, K. (1996). Data collected by MIPS on behalf of the European yeast chromosome VII sequencing project: TY3B gene product of Saccharomyces cerevisiae. [Direct submission to GenBank, Accession No. Z72894]
23. Hasegawa, A., Verver, J., Shimada, A., Saito, M., Goldbach, R., Van Kammern, A., Miki, K., Kameya-Iwaki, M., and Hibi, T. (1989). The complete sequence of soybean chlorotic mottle virus DNA and the identification of a novel promoter. Nucleic Acids Res. 17, 9993-10013.
24. Hay, J. M., Jones, M. C., Blakebrough, M. L., Dasgupta, I., Davies, J. W., and Hull, R. (1991). An analysis of the sequence of an infectious clone of rice tungro bacilliform virus, a plant pararetrovirus. Nucleic Acids Res. 19, 2615-2621.
25. Hearon, S. S., and Locke, J. C. (1984). Graft, pollen, and seed transmission of an agent associated with top spotting in Kalanchoe blossfeldiana. Plant Dis. 68, 347-350.
26. Hull, R., and Covey, S. N. (1996). Retroelements: Propagation and adaptation. Virus Genes 11, 105-118.
27. Hull, R., Sadler, J., and Longstaff, M. (1986). The sequence of carnation etched ring virus DNA: Comparison with cauliflower mosaic virus and retroviruses. EMBO J. 5, 3083-3090.
28. Kano, H., Koizumi, M., Noda, H., Hibino, H., Ishikawa, K., Omura, T., Cabauatan, P. Q., and Koganezawa, H. (1992). Nucleotide sequence of capsid protein gene of rice tungro bacilliform virus. Arch. Virol. 124, 157-163.
29. Khan, E., Mack, J. P. G., Katz, R. A., Kulkosky, J., and Skalka, A. M. (1991). Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 19, 851-860.
30. Kim, A., Terzian, C., Santamaria, P., Pelisson, A., Prud'homme, N., and Bucheton, A. (1994). Retrovirus in invertebrates: The gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91, 1285-1289.
31. Koonin, E. V., Mushegian, A. R., Ryabov, E. V., and Dolja, V. V. (1991). Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity. J. Gen. Virol. 72, 2895-2903.
32. Koshy, R., and Meyer, M. (1992). Oncogenicity of hepatitis B virus. Rev. Med. Virol. 2, 131-140.
33. Kulkosky, J., Jones, K. S., Katz, R. A., Mack, J. P. G., and Skalka, A. M. (1992). Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12, 2331-2338.
34. Lam, E., Benfey, P. N., Gilmartin, P. M., Fang, R., and Chua, N.-H. (1989). Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. Proc. Natl. Acad. Sci. USA 86, 7890-7894.
35. Lesemann, D.-E., and Casper, R. (1973). Electron microscopy of petunia vein-clearing virus, an isometric plant virus associated with specific inclusion in petunia cells. Phytopathology 63, 1118-1124.
36. Lockhart, B. E. L., and Olszewski, N. E. (1994). Badnaviruses. In "Encyclopedia of Virology" (R. G. Webster and A. Granoff, Eds.), Vol. 1, pp. 139-143. Academic Press, London/San Diego.
37. McClure, M. A. (1993). Evolutionary history of reverse transcriptase. In "Reverse Transcriptase," pp. 425-444. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
38. Medberry, S. L., Lockhart, B. E. L., and Olszewski, N. E. (1990). Properties of commelina yellow mottle virus's complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acids Res. 18, 5505-5513.
39. Menissier, J., de Murcia, G., Lebeurier, G., and Hirth, L. (1983). Electron microscopic studies of the different topological forms of the cauliflower mosaic virus DNA: Knotted encapsidated DNA and nuclear minichromosome. EMBO J. 2, 1067-1071.
40. Petrzik, K., Benes, V., Honetslegrova-Franova, J., Spak, J., and Ansorge, W. (1996). The sequence of strawberry vein-banding virus. [Direct submission to EMBL, Accession No. X97304]
41. Pique, M., Mougeot, J. L., Geldreich, A., Guidasci, T., Mesnard, J. M., Lebeurier, G., and Yot, P. (1995). Sequence of a cauliflower mosaic virus strain infecting solanaceous plants. Gene 155, 305-306.
42. Qu, R., Bhattacharyya, M., Laco, G. S., de Kochko, A., Subba Rao, B. L., Kaniewska, M. B., Elmer, J. S., Rochester, D. E., Smith, C. E., and Beachy, R. N. (1991). Characterization of the genome of rice tungro bacilliform virus: Comparison with commelina yellow mottle virus and caulimoviruses. Virology 185, 354-364.
43. Richert, K. R. (1993). Untersuchungen zur Charakterisierung des petunia vein-clearing virus (PVCV), ein samenübertragbares Pararetrovirus, pp. 45-54. Univ. of Göttingen, Germany. [Ph.D. Thesis]
44. Richert-Pöggeler, K. R., Shepherd, R. J., and Casper, R. (1996). Petunia vein-clearing virus, a pararetrovirus that also exists as a retroelement in the chromosome of its host. In "Abstract Book of Xth International Congress of Virology, Jerusalem, Israel," p. 16, W05-1.
45. Richins, R. D. (1994). Organization and transcription of the peanut chlorotic streak caulimovirus genome. [Direct submission to GenBank, Accession No. U13988]
46. Richins, R. D., and Shepherd, R. J. (1983). Physical maps of the genomes of dahlia mosaic virus and mirabilis mosaic virus - Two members of the caulimovirus group. Virology 124, 208-214.
47. Richins, R. D., Scholthof, H. B., and Shepherd, R. J. (1987). Sequence of figwort mosaic virus DNA (caulimovirus group). Nucleic Acids Res. 15, 8451-8466.
48. Rogers, S. O., and Bendich, A. J. (1988). Extraction of DNA from plant tissues. Plant Mol. Biol. Manual A6, 1-10.
49. Saigo, K., Kugimiya, W., Matsuo, Y, Inouye, S., Yoshika, K., and Yuki, S. (1984). Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster. Nature (London) 312, 659-661.
50. Sambrook, J., Fritsch, E. P., and Maniatis, T. (1989). "Molecular Cloning," 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
51. Sanger, F., Nicklen, S., and Coulsen, A. R. (1977). DNA sequencing with chain-termination inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463-5467.
52. Shepherd, R. J. (1994). Caulimoviruses. In "Encyclopedia of Virology" (R. G. Webster and A. Granoff, Eds.), Vol. 1, pp. 223-226. Academic Press, London/San Diego.
53. Smyth, D. R., Kalitsis, P., Joseph, J. L., and Sentry, J. W. (1989). Plant retrotransposon from Lilium henryi is related to Ty3 of yeast and the gypsy group of Drosophila. Proc. Natl. Acad. Sci. USA 86, 5015-5019.
54. Song, S. U., Gerasimova, T., Kurkulos, M., Boeke, J. D., and Corces, V. G. (1994). An env-like protein encoded by a Drosophila retroelement: Evidence that gypsy is an infectious retrovirus. Genes Dev. 8, 2046-2057.
55. Southern, E. M. (1975). Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503-517.
56. Toh, H., Kikuno, R., Hayashida, H., Miyata, T., Kugimiya, W., Inouye, S., Yuki, S., and Saigo, K. (1985). Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus. EMBO J. 4, 1267-1272.
57. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
58. van Gent, D. C., Oude Groeneger, A. A. M., and Plasterk, R. H. A. (1992). Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc. Natl. Acad. Sci. USA 89, 9598-9602.
59. Weaver, D. C., Shpakovski, G. V., Caputo, E. Levin, H. L., and Boeke, J. D. (1993). Sequence analysis of closely related retrotransposon families from fission yeast. Gene 131, 135-139.
60. Xiong, Y., and Eickbush, T. H. (1990). Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9, 3353-3362.