1887

Abstract

Phylogenetic analyses based on baculovirus polyhedrin nucleotide and amino acid sequences revealed two major nucleopolyhedrovirus (NPV) clades, designated Group I and Group II. Subsequent phylogenetic analyses have revealed three Group II subclades, designated A, B and C. Variations in amino acid frequencies determine the extent of dissimilarity for divergent but structurally and functionally conserved genes and therefore significantly influence the analysis of phylogenetic relationships. Hence, it is important to consider variations in amino acid codon usage. The Genome Hypothesis postulates that genes in any given genome use the same coding pattern with respect to synonymous codons and that genes in phylogenetically related species generally show the same pattern of codon usage. We have examined codon usage in six genes from six NPVs and found that: (1) there is significant variation in codon use by genes within the same virus genome; (2) there is significant variation in the codon usage of homologous genes encoded by different NPVs; (3) there is no correlation between the level of gene expression and codon bias in NPVs; (4) there is no correlation between gene length and codon bias in NPVs; and (5) that while codon use bias appears to be conserved between viruses that are closely related phylogenetically, the patterns of codon usage also appear to be a direct function of the GC-content of the virus-encoded genes.

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2000-09-01
2024-12-04
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References

  1. Ahrens C. H., Russell R. L., Funk C. J., Evans J. T., Harwood S. H., Rohrmann G. F. 1997; The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 229:381–399
    [Google Scholar]
  2. Ayres M. D., Howard S. C., Kuzio J., Lopez-Ferber M., Possee R. D. 1994; The complete DNA sequence of Autographa californica nuclear polyhedrosis virus. Virology 202:586–605
    [Google Scholar]
  3. Bennetzen J. L., Hall B. D. 1982; Codon selection in yeast. Journal of Biological Chemistry 257:3026–3031
    [Google Scholar]
  4. Blissard G. W., Rohrmann G. F. 1990; Baculovirus diversity and molecular biology. Annual Review of Entomology 35:127–155
    [Google Scholar]
  5. Bronson C. B., Anderson J. N. 1994; Nucleotide composition as a driving force in the evolution of retroviruses. Journal of Molecular Evolution 38:506–532
    [Google Scholar]
  6. Bulach D. M., Kumar A., Zaia A., Liang B., Tribe D. E. 1999; Group II nucleopolyhedrovirus subgroups revealed by phylogenetic analyses of polyhedrin and DNA polymerase gene sequences. Journal of Invertebrate Pathology 73:59–73
    [Google Scholar]
  7. Carstens E., Tija S. T., Doerfler W. 1979; Infection of Spodoptera frugiperda cells with Autographa californica nuclear polyhedrosis virus. I. Synthesis of intracellular proteins after infection. Virology 99:386–398
    [Google Scholar]
  8. Cowan P., Bulach D., Goodge K., Robertson A., Tribe D. E. 1994; Nucleotide sequence of the polyhedrin gene of Helicoverpa zea single nucleocapsid nuclear polyhedrosis virus: placement of the virus in lepidopteran nuclear polyhedrosis virus group II. Journal of General Virology 75:3211–3218
    [Google Scholar]
  9. Croizier L., Croizier G. 1994; Nucleotide sequence of the polyhedrin gene of Spodoptera littoralis multiple nucleocapsid nuclear polyhedrosis virus. Biochimica et Biophysica Acta 1218:457–459
    [Google Scholar]
  10. Faktor O., Toister-Achituv M., Nahum O. 1997a; Enhancer element, repetitive sequences and gene organization in an 8-kbp region containing the polyhedrin gene of the Spodoptera littoralis nucleopolyhedrovirus. Archives of Virology 142:1–15
    [Google Scholar]
  11. Faktor O., Toister-Achituv M., Nahum O., Kamensky B. 1997b; The p10 gene of Spodoptera littoralis nucleopolyhedrovirus: nucleotide sequence, transcriptional analysis and unique gene organization in the p10 locus. Journal of General Virology 78:2119–2128
    [Google Scholar]
  12. GenBank. 1999; Codon Count Program 112.0. Codon Usage Database released by GenBank. http://www.kazusa.or.jp/codon
  13. Gouy M., Goutier C. 1982; Codon useage in bacteria: correlation with expressivity. Nucleic Acids Research 10:7055–7074
    [Google Scholar]
  14. Halpern A. L., Bruno W. J. 1998; Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Molecular Biology and Evolution 15:910–917
    [Google Scholar]
  15. Hu Z. H., Broer R., Westerlaken J., Martens J., Jin F., Jehle J. A., Wang L. M., Vlak J. M. 1997; Characterization of the ecdysteroid UDP-glycosyltransferase gene of a single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria . Virus Research 47:91–97
    [Google Scholar]
  16. Ikemura T. 1985; Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution 2:13–34
    [Google Scholar]
  17. Kuzio J., Pearson M. N., Harwood S. H., Funk C. J., Evans J. T., Slavicek J. M., Rohrmann G. F. 1999; Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar . Virology 253:17–34
    [Google Scholar]
  18. Li W.-H. 1997 Molecular Evolution , 2nd edn. Sunderland, MA: Sinauer Associates;
  19. Ooi B. G., Miller L. K. 1988; Regulation of host RNA levels during baculovirus infection. Virology 166:515–523
    [Google Scholar]
  20. O’Reilly D. R., Miller L. K., Lucknow V. A. 1992 Baculovirus Expression Vectors: A Laboratory Manual New York: W. H. Freeman;
  21. Powell J. R., Moriyama E. N. 1997; Evolution of codon bias in Drosophila . Proceedings of the National Academy of Sciences, USA 94:7784–7790
    [Google Scholar]
  22. Ranjan A., Hasnain S. E. 1994; Influence of codon usage and translation initiation context in the AcMNPV-based expression system: computer analysis using homologous and heterologous genes. Virus Genes 9:149–153
    [Google Scholar]
  23. Ranjan A., Hasnain S. E. 1995; Codon usage in the prototype baculovirus: Autographa californica nuclear polyhedrosis virus. Indian Journal of Biochemistry and Biophysics 32:424–428
    [Google Scholar]
  24. Sharp P. M., Li W. H. 1987; An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution 24:28–38
    [Google Scholar]
  25. Shields D. C., Sharp P. M., Higgins D. G., Wright F. 1988; Silent sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution 5:704–716
    [Google Scholar]
  26. Stoler M. H., Rhodes C. R., Whitbeck A., Wollinsky S. M., Chow L. T., Broker T. R. 1992; Human papillomavirus type 16 and 18 genes expression in cervical neoplasias. Human Pathology 23:117–128
    [Google Scholar]
  27. van Hemert F. J., Berkhout B. 1995; The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability. Journal of Molecular Evolution 41:132–140
    [Google Scholar]
  28. Volpers C., Schirmacher P., Streek E., Sapp M. 1994; Assembly of the major and the minor capsid protein of human papillomavirus type 33 into virus-like particles and tubular structures in insect cells. Virology 200:504–512
    [Google Scholar]
  29. Wright F. 1990; The ‘effective number of codons’ used in a gene. Gene 87:23–29
    [Google Scholar]
  30. Zanotto P. M., Kessing B. D., Maruniak J. E. 1993; Phylogenetic relationships among baculoviruses: evolutionary rates and host associations. Journal of Invertebrate Pathology 62:47–164
    [Google Scholar]
  31. Zhou J., Liu W. J., Peng S. W., Sun X. Y., Fraser I. 1999; Papillomavirus capsid protein expression depends on a match between codon usage and tRNA availability. Journal of Virology 73:4972–4982
    [Google Scholar]
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