Sequence, function, and phylogenetic analysis of an ascovirus DNA polymerase gene

Virology

Volumn 216, Issue 1, 1996, Pages 146-157

  Pellock, Brett J ^a   Lu, Albert ^a   Meagher, Richard B ^a   Weise, Michael J ^b   Miller, Lois K ^a,c  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; DNA VIRUS; GENETIC ANALYSIS; INSECT; LEPIDOPTERA; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VIRUS CLASSIFICATION;

EID: 0029928133     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.1996.0041     Document Type: Article

References (72)

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. Avery, S. W., Jouvenaz, D. P., Banks, W. A., and Anthony, D. W. (1977). Virus-like particles in a fire ant, Solenopsis sp. (Hymenoptera: Formicidae) from Brazil. Fl. Entomol. 60, 17-20.
3. Baer, R., Bankier, A. T., Biggin, M. D., Deininger, P. L., Farrel, P. J., Gibson, T. J., Hatful, G., Hudson, G. S., Satchwell, S. C., Seguin, C., Tuffnell, P. S., and Barrell, B. G. (1984). DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310, 207-211.
4. Bernad, A., Zaballos, A, Salas, M., and Blanco, L. (1987). Structural and functional relationships between procaryotic and eukaryotic DNA polymerases. EMBO J. 6, 4219-4225.
5. Bernad, A., Blanco, L., Lazaro, J. M., Martin, G., and Salas, M. (1989). A conserved 3′-5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59, 219-228.
6. Binns, M. M., Stenzler, L., Tomley, F. M., Campbell, J., and Boursnel, M. B. G. (1987). Identification by a random sequencing strategy of the fowlpoxvirus DNA polymerase gene, its nucleotide sequence and comparison with other viral DNA polymerases. Nucleic Acids Res. 15, 6563-6573.
7. Bonner, C. A., Hays, S., McEntee, K., and Goodman, M. F. (1990). DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 87, 7663-7667.
8. Boulet, A., Simon, M., Faye, G., Bauer, G. A., and Burgers, P. M. J. (1989). Structure and function of the Saccharomyces cerevisiae CDC2 gene encoding the large subunit of DNApolymerase III. EMBO J. 8, 1849-1854.
9. Braithewaite, D. K., and Ito, J. (1993). Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 21, 787-802.
10. Browning, H. W., Federici, B. A., and Oatman, E. R. (1982). Occurrence of a disease caused by a Rickettsia-like organism in a larval population of the cabbage looper, Trichoplusia ni, in southern California. Environ. Entomol. 11, 550-554.
11. Carner, G. R. and Hudson, J. S. (1983). Histopathology of virus-like particles in Heliothis spp. J. Invertebr. Path. 41, 238-249.
12. Chaeychomsri, S., Ikeda, M., and Kobayashi, M. (1995). Nucleotide sequence and transcriptional analysis of the DNA polymerase gene of Bombyx mon nuclear polyhedrosis virus. Virology 206, 435-447.
13. Damagnez, V., Tillit, J., de Recondo, A., and Baldacci, G. (1991). The POL1 gene from the fission yeast, Schizosaccharomyces pombe, shows conserved amino acid blocks specific for eukaryotic DNA polymerases alpha. Mol. Gen. Genet. 226, 182-189.
14. Dekker, B. M. M., and van Ormondt, H. (1984). The nucleotide sequence of fragment HindIII-C of human adenovirus type 5 DNA. Gene. 27, 115-120.
15. Earl, P. L., Jones, E. V., and Moss, B. (1986). Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: Nucleotide sequence of the vaccinia virus DNA polymerase gene. Proc. Natl. Acad. Sci. USA 83, 3659-3663.
16. Engler, J. A., Hoppe, M. S., and van Bree, M. P. (1983). The nucleotide sequence of the genes encoded in early region 2b of human adenovirus type 7. Gene 21, 145-159.
17. Federici, B. A. (1982). A new type of insect pathogen in larvae of the clover cutworm, Scotogramma trifolii. J. Invert. Pathol. 40, 41-54.
18. Federici, B. A. (1983). Enveloped double stranded DNA insect virus with novel structure and cytopathology. Proc. Natl. Acad. Sci. 80, 7664-7668.
19. Federici, B. A. (1993). Viral pathobiology in relation to insect control. In "Parasites and Pathogens of Insects" (N. E. Beckage, S. N. Thompson, and B. A. Federici, Eds.), Vol 2, pp. 81-101. Academic Press, San Diego.
20. Federici, B. A. (1994). Ascoviruses. In "Encyclopedia of Virology" (R. G. Webster and A. Granoff, Eds.), Vol. 1, pp.58-63. Academic Press, London/San Diego.
21. Federici, B. A., and Govindarajan, R. (1990). Comparative histopathology of three ascovirus isolates in larval noctuids. J. Invertebr. Pathol. 56, 300-311.
22. Federici, B. A., Vlak, J. M., and Hamm, J. J. (1990). Comparative study of virion structure, protein composition and genomic DNA of three ascovirus isolates. J. Gen. Virol. 71, 1661-1668.
23. Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package) Version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle, WA.
24. Genetics Computer Group (1994). "Program Manual for the Wisconsin Package," Version 8, Genetics Computer Group, 575 Science Drive, Madison, WI, 53771.
25. Gibbs, J. S., Chiou, H. C., Hall, J. D., Mount, D. W., Retondo, M. J., Weller, S. J., and Coen, D. M. (1985). Sequence and mapping analyses of the herpes simplex virus DNA polymerase gene predict a C-terminal substrate binding domain. Proc. Natl. Acad. Sci. USA 82, 7969-7973.
26. Gingeras, T. R., Sciaky, D., Gelinas, R. E., Bing-Dong, J., Yen, C. E., Kelly, M. M., Bullock, P. A., Parsons, B. L., O'Neill, K. E., and Roberts, R. J. (1982). Nucleotide sequences from the adenovirus 2 genome. J. Biol. Chem. 257, 13475-13491.
27. Gorman, C. M., Moffat, L. F., and Howard, B. H. (1982). Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol. Cell Biol. 2, 1044-1051.
28. Govindarajan, R., and Federici, B. A. (1990). Ascovirus infectivity and effects of infection on the growth and development of noctuid larvae. J. Invertebr. Pathol. 56, 291-299.
29. Grabherr, R., Strasser, P., and Van Etten, J. L. (1992). The DNA polymerase gene from chlorella viruses PBCV-1 and NY-2A contains an intron with nuclear splicing sequences. Virology 188, 721-731.
30. Hamm, J. J., Nordlund, D. A., and Marti, O. G. (1985). Effects of a nonoccluded virus of Spodoptera frugiperda (Lepidoptera: Noctuidae) on the development of a parasitoid, Cotesia marginiventris (Hymenoptera: Braconidae). Environ. Entomol. 14, 258-261.
31. Hamm, J. J., Pair, S. D., and Marti, O. G. (1986). Incidence and host range of a new ascovirus isolated from fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae). Fl. Entomol. 69, 524-531.
32. Henikoff, S. (1987). Unidirectional digestion with exonuclease III in DNA sequence analysis. Methods Enzymol. 155, 156.
33. Hirose, F., Yamaguchi, M., Nishida, Y., Masutani, M., Miyazawa, H., Hanaoka, F., and Matsukage, A. (1991). Structure and expression during development of Drosophila melanogaster gene for DNA polymerase alpha. Nucleic Acids Res. 19, 4991-4998.
34. Jung, G., Leavitt, M. C., Hsieh, J., and Ito, J. (1987). Bacteriophage PRD1 DNA polymerase: Evolution of DNA polymerases. Proc. Natl. Acad. Sci. USA 84, 8287-8291.
35. Kempken, F., Meinhardt, F., and Esser, K. (1989). In organello replication and viral affinity of linear, extrachromosomal DNA of the ascomycete Ascolobus immersus. Mol. Gen. Gen. 218, 523-530.
36. Kouzarides, T., Bankier, A. T., Satchwell, S. C., Weston, K., Tomlinson, P., and Barrel, B. G. (1987). Sequence and transcription analysis of the human cytomegalovirus DNA polymerase gene. J. Virol. 61, 125-133.
37. Larder, B. A., Kemp, S. D., and Darby, G. (1987). Related functional domains in virus DNA polymerases. EMBO J. 6, 169-175.
38. Leegwater, P. A. J., Strating, M., Murphy, N. B., Kooy, R. F., van der Vliet, P. C., and Overdulve, J. P. (1991). The Trypanosoma brucei DNA polymerase alpha core subunit gene is developmentally regulated and linked to a constitutively expressed open reading frame. Nucleic Acids Res. 19, 6441-6447.
39. Lu, A. L., and Miller, L. K. (1994). Identification of three late expression factor genes within the 33.8 to 43.4 map unit region of Autograpa californica nuclear polyhedrosis virus (AcMNPV). J. Virol. 68, 6710-6718.
40. Lu, A. L., and Miller, L. K. (1995). The roles of eighteen baculovirus late expression factor genes in transcription and DNA replication. J. Virol. 69, 975-982.
41. Manniatis, T., Fritsch, E. F., and Sambrook, J. (1989). "Molecular Cloning: A Laboratory Manual." Cold Spring Harbor Laboratory, Cold Spring Harbor NY.
42. Marti, O. G., Hamm, J. J., and Styer, E. L. (1987). Discharge of hemolymph from the ventral eversible gland of ascovirus-infected fall armyworm larvae, Spodoptera frugiperda (Lepidoptera: Noctuidae). J. Invertebr. Pathol. 49, 127-129.
43. Mathur, E. J., Adams, M. W. W., Callen, W. N., and Cline, J. M. (1991). The DNA polymerase gene from the hyperthermophilic marine archaebacterium, Pyrococcus furiosis, shows sequence homology with alpha-like DNA polymerases. Nucleic Acids Res. 19, 6952.
44. Matsumoto, K., Takano, Hiroyoshi, Kim, C. I., and Hirokawa, Hideo. (1989). Primary structure of bacteriophage M2 DNA polymerase: Conserved segments within protein-priming DNA polymerases and DNA polymerase I of Escherichia coli. Gene 84, 247-255.
45. Morrison, A., Bell, J. B., Kunkel, T. A., and Sugino, A. (1991). Eukaryotic DNA polymerase amino acid sequence required for 3′-5′ exonuclease activity. Proc. Natl. Acad. Sci. USA 88, 9473-9477.
46. Mustafa, A., and Yuen, L. (1991). Identification and sequenceing of the Choristoneura biennis entomopoxvirus DNA polymerase gene. DNA Sequence 2, 39-45.
47. Oeser, B., and Tudzynski, P. (1989). The linear mitochondrial plasmid pCIKI of the phytopathogenic fungus Claviceps purpurea may code for a DNA polymerase and an RNA polymerase. Mol. Gen. Genet. 217, 132-140.
48. O'Reilly, D. R., Miller, L. K., and Luckow, V. A. (1992). "Baculovirus Expression Vectors: A Laboratory Manual." Freeman, New York.
49. Paillard, M., Sederoff, R. R., and Levings, C. S. (1985). Nucleotide sequence of the S-1 mitochondrial DNA from the cytoplasm of maize. EMBO J. 4, 1125-1128.
50. Passarelli, A. L., and Miller L. K. (1993). Three baculovirus genes in-volved in late and very late gene expression: ie-I, ien, and lef-2. J. Virol. 67, 2149-2158.
51. Pearson, M. R., Bjornson, R., Pearson, G., and Rohrmann, G. (1992). The Autographa californica baculovirus genome: Evidence for multiple replication origins. Science 257, 1382-1384.
52. Pearson, W. R., and Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
53. Perler, F. B., Comb, D. G., Jack, W. E., Moran, L. S., Qiang, B., Kucera, R. B., Benner, J., Satsko, B. E., Nwankwo, D. O., Hempstead, S. K., Carlow, C. K. S., and Jannasch, H. (1992). Intervening sequences in an Archaea DNA polymerase gene. Proc. Natl. Acad. Sci. USA 89, 5577-5581.
54. Pignede, G., Bouvier, D., de Recondo, A., and Baldacci, G. (1991). Characterization of the POL3 gene product from Schizosaccharomyces pombe indicates inter-species conservation of the catalytic subunit of DNA polymerase delta. J. Mol. Biol. 222, 209-218.
55. Pisani, F. M., Martino, C. D., and Rossi, M. (1992). A DNA polymerase from the archaeon Sulfolobus solfataricus shows sequence similarity to family B DNA polymerases. Nucleic Acids Res. 20, 2711-2716.
56. Pizzagalli, A., Valsasnini, P., Plevani, P, and Lucchini, G. (1988). DNA polymerase I gene of Saccharomyces cerevisiae: Nucleotide sequence, mapping of temperature-sensitive mutation, and protein homology with other DNA polymerases. Proc. Natl. Acad. Sci. USA 85, 3772-3776.
57. Ridley, R. G., White, J. H., McAleese, S. M., Goman, M., Alano, P., deVries, E., and Kilbey, B. J. (1991). DNA polymerase delta: Gene sequences from Plasmodium falciparum indicate that this enzyme is more highly conserved than DNA polymerase alpha. Nucleic Acids Res. 19, 6731-6736.
58. Rodriguez, J. M., Yanez, R. J., Rodriguez, J. F., Vinuela, E., and Salas, M. L. (1993). The DNA polymerase-encoding gene of African swine fever virus: Sequence and transcriptional analysis. Gene 136, 103-110.
59. Shu, L., Hong, J. S., Wei, Y., and Engler, J. A. (1986). Nucleotide sequence of the genes encoded in early region 2b of human adenovirus 12. Gene 46, 187-195.
60. Spicer, E. K., Rush, J., Fung, C., Reha-Krantz, L. J., Karam, J. D., and Konigsberg, W. H. (1988). Primary structure of the T4 DNA polymerase. J. Biol. Chem. 263, 7478-7486.
61. Stark, M. J. R., Mileham, A. J., Romanos, M. A., and Boyd, A. (1984). Nucleotide sequence and transcription analysis of a linear DNA plasmid associated with the killer character of the yeast Kluyveromyces lactis. Nucleic Acids Res. 12, 6011-6030.
62. Thiem, S. M., and Miller, L. K. (1990). Differential gene expression mediated by late, very late, and hybrid baculovirus promotors. Gene 91, 87-94.
63. Todd, J. W., Passarelli, A. L., and Miller, L. K. (1995). Bghteen baculovirus genes, including lef-11, p35, 39K, and p47 support late gene expression. J. Virol. 69, 968-974.
64. Tomalski, M., Wu, J., and Miller, L. K. (1988). The location, sequence, transcription, and regulation of a baculovirus DNA polymerase gene. Virology 167, 591-600.
65. Tommasino, M., Ricci, S., and Galeotti, C. L. (1988). Genome organization of the killer plasmid pGK12 from Kluyveromyces lactis. Nucleic Acids Res. 16, 5863-5878.
66. Uemori, T., Ishino, Y., Toh, H., Asada, K., and Kato, I. (1993). Organization and nucleotide sequence of the DNA polymerase gene from the archaeon Pyrococcus furiosis. Nucleic Acids Res. 21, 259-265.
67. Vaughn, J. L., Goodwin, R. H., Thompkins, G. L., and McCawley, P. (1977). The establishment of two cell lines from the insect Spodoptera frugiperda (Lepidoptera: Noctuidae). In Vitro 13, 213-217.
68. Wang, T. S.-F., Wong, S. W., and Korn, D. (1989). Human DNA polymerase alpha: Predicted functional domains and relationships with viral DNA polymerases. FASEB J. 3, 14-21.
69. Wong, S. W., Wahl, A. F., Yuan, P., Arai, N., Pearson, B. E., Arai, K., Korn, D., Hunkapiller, M. W., and Wang, T. S.-F. (1988). Human DNA polymerase alpha gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO J. 7, 37-47.
70. Yang, C., Chang, L., Zhang, P., Hao, H., Zhu, L., Toomey, N. L., and Marietta Y. W. T. L. (1992). Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase delta. Nucleic Acids Res. 20, 735-745.
71. Yoshikawa, H., and Ito, J. (1982). Nucleotide sequence of the major early region of bacteriophage Phi 29. Gene 17, 323-335.
72. Zang, J., Chung, D. W., Tan, C., Downey, K. M., Davie, E. W., and So, A. G. (1991). Primary structure of the catalytic subunit of calf thymus DNA polymerase delta: Sequence similarities with other DNA polymerases. Biochemistry 30, 11742-11750.