The DNA polymerase gene of a brown algal virus: Structure and phylogeny

Journal of Phycology

Volumn 34, Issue 4, 1998, Pages 608-615

  Lee, Amy M ^a   Ivey, Richard G ^a   Meints, Russel H ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

Brown algae; DNA polymerase; Feldmannia sp.; FsV 1; Phaeophyceae; Phylogeny; Virus

Indexed keywords

BROWN ALGAL VIRUS; CODON; DNA POLYMERASE; DNA SYNTHESIS; ENZYME STRUCTURE; GENE SEQUENCING;

FELDMANNIA;

EID: 0031659932     PISSN: 00223646     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.1998.340608.x     Document Type: Article

References (45)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-10.
2. Baer, R. J., Bankier, A. T., Biggin, M. D., Deininger, P. L., Farrell, P. J., Gibson, T. J., Hatfull, G. F., Hudson. G. S., Satchwell, S. C., Seguin, C., Tuffnell, P. S. & Barrell, B. G. 1984. DNA sequence and expression of the B95-8 Epstein-Barr genome. Nature 310:207-11.
3. Berthomme, H., Monahan, S. J., Parris, D. S., Jacquemont, B. & Epstein, A. L. 1995. Cloning, sequencing, and functional characterization of the two subunits of the pseudorabies virus DNA polymerase holoenzyme: evidence for specificity of interaction. J. Virol. 69:2811-8.
4. Binns, M. M., Stezier, L., Tomley, F. M., Campbell, J. & Boursnell, M. E. 1987. Identification by a random sequencing strategy of the fowlpox virus DNA polymerase gene, its nucleotide sequence and comparison with other viral DNA polymerases. Nucleic Acids Res. 15:6563-73.
5. Bjornson, R. M., Glocker, B. & Rochrmann, G. F. 1992. Characterization of the nucleotide sequence of the Lymantria dispar nuclear polyhedrosis virus DNA polymerase gene region. J. Gen. Virol. 73:3177-83.
6. Braithwaite, D. K. & Ito, J. 1993. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 21:787-802.
7. Chen, F. & Suttle, C. A. 1995. Amplification of DNA polymerase gene fragments from viruses infecting microalgae. Appl. Environ. Microbiol. 61:1274-8.
8. _ 1996. Evolutionary relationships among large double-stranded DNA viruses that infect microalgae and other organisms as inferred from DNA polymerase genes. Virology 219:170-8.
9. Cowan, P., Bulach, D., Goodge, K., Robertson, A. & Tribe, D. E. 1994. Nucleotide sequence of the polyhedrin gene region of the Helicoverpa zae single nucleocapsid nuclear polyhedrosis virus: placement of the virus in lepidopteran nuclear polyhedrosis virus group II. J. Gen. Virol. 75:3211-8.
10. Davison, A. J. & Scott, J. E. 1986. The complete DNA sequence of varicella-zoster virus. J. Gen. Virol. 67:1759-1816.
11. Devereux, J., Haeberli, P. & Smithies, O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-95.
12. Earl, P. L., Jones, E. V. & Moss, B. 1986. Homology between DNA polymerase of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene. Proc. Natl. Acad. Sci. USA 83:3659-63.
13. Elliot, R., Clark, C., Jaquish, D. & Spector, D. H. 1991. Transcription analysis and sequence of the putative Murine cytomegalovirus DNA polymerase gene. Virology 185:169-86.
14. Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-65.
15. _ 1993. PHYLIP-Phylogeny inference package, version 3.5. Department of Genetics, University of Washington, Seattle.
16. _ 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266:418-27.
17. Friess-Klebl, A.-K., Knippers, R. E. & Müller, D. G. 1994. Isolation and characterization of a DNA virus infecting Feldmannia simplex (Phaeophyceae). J. Phycol. 30:653-8.
18. Grabherr, R., Strasser, P. & 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: 721-31.
19. Graves, M. V. & Meints, R. H. 1992a. Characterization of the gene encoding the most abundant in vitro translation product from virus-infected Chlorella-like algae. Gene 113:149-55.
20. _ 1992b. Characterization of the major capsid protein and cloning of its gene from algal virus PBCV-1. Virology 188:198-207.
21. Henry, E. C. & Meints, R. H. 1992. A persistent virus infection in Feldmannia (Phaeophyceae). J. Phycol. 28:517-26.
22. Higgins, D. G. 1994. CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol. Biol. 25:307-18.
23. Hillis, D. M. & Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-92.
24. Ito, J. & Braithwaite, D. K. 1991. Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res. 19:4045-57.
25. Ivey, R. G., Henry, E. C., Lee, A. M., Klepper, L., Krueger, S. K. & Meints, R. H. 1996. A Feldmannia algal virus has two genome size-classes. Virology 220:267-73.
26. Kouzarides, T., Bankier, A. T., Satchwell, S. C. & Weston, K. 1987. Sequence and transcription analysis of the human cytomegalovirus DNA polymerase gene. J. Virol. 61:125-33.
27. Krueger, S. K., Key, R. G., Henry, E., C. & Meints, R. H. 1996. A 4.5 kbp nucleotide sequence fragment from a large ds-DNA brown algal virus contains ORFs and a "RING" zinc finger motif. Virology 219:301-3.
28. Lanka, S. T., Klein, M., Ramsperger, U., Müller, D. G. & Knippers, R. 1993. Genome structure of a virus infecting the marine brown alga Ectocarpus siliculosis. Virology 193:802-11.
29. Larder, B. A., Kemp, S. D. & Darby, G. 1987. Related functional domains in virus DNA polymerases. EMBO J. 6:169-75.
30. Lee, A. M., Ivey, R. G., Henry, E. C. & Meints, R. H. 1995. Characterization of a repetitive DNA element in a brown algal virus. Virology 212:474-80.
31. Mao, J., Hedrick, R. P. & Chinchar, V. G. 1997. Molecular characterization, sequence analysis, and taxonomic position of newly isolated fish Iridoviruses. Virology 229:212-20.
32. Martins, A., Ribeiro, G., Marques, M. I. & Costa, J. V. 1994. Genetic identification and nucleotide sequence of the DNA polymerase gene of African swine fever virus, Nucleic Acids Res. 22:208-13.
33. Meints, R. H., Lee, K., Burbank, D. E. & Van Etten, J. L. 1984. Infection of a Chlorella-like alga with the virus, PBCV-1: ultra-structural studies. Virology 138:341-6.
34. Müller, D. G. 1991. Mendelian segregation of a virus genome during host meiosis in the marine brown alga Ectocarpus siliculosis. J. Plant Physiol. 137:739-43.
35. Müller, D. G., Brautigam, M. & Knippers, R. 1996. Virus infection and persistence of foreign DNA in the marine brown alga Feldmannia simplex (Ectocarpels, Phaeophyceae). Phycologia 35:61-3.
36. Müller, D. G. & Frenzer, K. 1993. Virus infections in three marine brown algae: Feldmannia irregularis, F. simplex, and Ectocarpus siliculosus. Hydrobiologia 260/261:37-14.
37. Müller, D. G., Kawai, H., Stache, B. & Lanka, S. 1989. A virus infection in the marine brown alga Ectocarpus siliculosus (Phaeophvceae). Bot. Acta 103:72-82.
38. Mustafa, A. & Yuen, L. 1991. Identification and sequencing of the Choristoneura biennis entomopoxvirus DNA polymerase gene. DNA Seq. 2:39-45.
39. Rohozinski, J., Girton, L. E. & Van Etten, J. L. 1989. Chlorella viruses contain linear nonpermuted double-stranded DNA genomes with covalently closed hairpin ends. Virology 168: 363-9.
40. Schleiss, M. R. 1994. Cloning and characterization of the guinea pig cytomegalovirus glycoprotein B gene. Virology 202:173-85.
41. Tidona, C. A. & Darai, G. 1997. The complete DNA sequence of Lymphocystis Disease Virus. Virology 230:207-16.
42. Tomalski, M. D., Wu, J. & Miller, L. K. 1988. The location, sequence, transcription, and regulation of a baculovirus DNA polymerase gene. Virology 167:591-600.
43. Tsurumi, T., Maeno, K. & Nishiyama, Y. 1987. Nucleotide sequence of the DNA polymerase gene of herpes simplex virus type-2 and comparison with the type-1 counterpart. Gene 52: 129-37.
44. Van Etten, J. L., Lane, L. C. & Meints, R. H. 1991. Viruses and viruslike particles of eukaryotic algae. Microbiol. Rev. 55:586-620.
45. Yuen, L. & Moss, B. 1987. Oligonucleotide sequence signaling transcriptional termination of Vaccinia virus early genes. Proc. Natl. Acad. Sci. USA 84:6417-21.