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Codon usage and bias among individual genes of the coccidia and piroplasms

Published online by Cambridge University Press:  06 April 2009

J. T. Ellis ,
D. A. Morrison ,
D. Avery  and
A. M. Johnson
J. T. Ellis
Affiliation:
Department of Microbiology, University of Technology Sydney, St Leonards Campus, P.O. Box 123 Broadway, New South Wales 2007, Australia
D. A. Morrison
Affiliation:
Department of Applied Biology, University of Technology Sydney, St Leonards Campus, P.O. Box 123 Broadway, New South Wales 2007, Australia
A. M. Johnson
Affiliation:
Department of Microbiology, University of Technology Sydney, St Leonards Campus, P.O. Box 123 Broadway, New South Wales 2007, Australia
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Summary

Codon usage has been analysed in individual gene sequences, derived from a variety of parasitic protozoa in the class Sporozoa of the phylum Apicomplexa using metric multidimensional scaling. The two groups of codon usage patterns detected reflect the two main subgroups of organisms studied (the coccidia and the piroplasms), and it is the pattern usage of synonymous codons that has the largest influence on overall codon usage in the individual genes, rather than being the pattern of amino acid composition of the gene product. The magnitude of the codon usage bias in the sequences was determined using three commonly used indices – NC', GC3s and B. In general, although relatively low levels of codon usage bias were detected in these gene sequences, codon usage bias does explain at least some of the codon usage patterns observed. Codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were either over-or under-represented in the nucleotide sequences. keeping with observations on prokaryotic organisms, it is speculated that the codon usage patterns detected in these parasitic protozoa are the result of directional mutation pressure on the base composition of the genomic DNA.

Keywords

BabesiaEimeriaTheileriaToxoplasmapiroplasmscoccidiacodon usage
Type
Research Article
Information
Parasitology , Volume 109 , Issue 3 , September 1994 , pp. 265 - 272
Copyright
Copyright © Cambridge University Press 1994

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References

REFERENCES

Anderson, D., McCandliss, R. J., Strausberg, S. L. & Strausberg, R. L. (1990). Genetically engineered coccidiosis vaccine. Patent Corporation Treaty W090/00403.Google Scholar
Andersson, S. G. E. & Kurland, C. G. (1990). Codon preferences in free-living micro-organisms. Microbiology Reviews 54, 198–210.CrossRefGoogle Scholar
Belbin, L. (1989). PATN – Pattern Analysis Package Technical Reference. Canberra: CSIRO.Google Scholar
Bernardi, G. & Bernardi, G. (1985). Codon usage and genome composition. Journal of Molecular Evolution 22, 363–5.CrossRefGoogle ScholarPubMed
Danforth, H. D., Augustine, P. C., Ruff, M. D., McCandliss, R., Strausberc, R. L. & Likel, M. (1989). Genetically engineered antigen confers partial protection against avian coccidial parasites. Poultry Science 68, 1643–52.CrossRefGoogle ScholarPubMed
Devereux, J., Haeberli, P. & Smithies, O. (1985). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12, 216–23.Google Scholar
Ellis, J., Griffin, H., Morrison, D. & Johnson, A. M. (1993). Analysis of dinucleotide frequency and codon usage in the phylum Apicomplexa. Gene 126, 163–70.CrossRefGoogle ScholarPubMed
Faith, D. P., Minchin, P. R. & Belbin, L. (1987). Compositional dissimilarity as a robust measure of ecological distances: a theoretical model and computer simulations. Vegetatio 69, 57–68.CrossRefGoogle Scholar
Hyde, J. E. & Sims, P. F. G. (1987). Anomalous dinucleotide frequencies in both coding and non-coding regions from the genome of the human malaria parasite Plasmodium falciparum. Gene 61, 177–87.CrossRefGoogle ScholarPubMed
Irwin, A. D. (1987). Characterisation of species and strains of Theileria. Advances in Parasitology 26, 145–97.Google Scholar
Johnson, A. M., Dubey, J. P. & Dame, J. B. (1986). Purification and characterisation of Toxoplasma gondii tachyzoite DNA. Australian Journal of Experimental Biology and Medical Science 64, 351–5.CrossRefGoogle ScholarPubMed
Levine, N. D. (1985). Phylum II. Apicomplexa Levine, 1970. In Illustrated Guide to the Protozoa (ed. Lee, J. J., Hutner, S. H. & Bovee, E. C.), pp. 322–374. Kansas: Society of Protozoologists.Google Scholar
Lloyd, A. T. & Sharp, P. M. (1992 a). Codons: a microcomputer program for codon usage analysis. Journal of Heredity 83, 239–40.CrossRefGoogle ScholarPubMed
Lloyd, A. T. & Sharp, P. M. (1992 b). Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Research 20, 5289–95.CrossRefGoogle ScholarPubMed
Long, M. & Gillespie, J. H. (1991). Codon usage divergence of homologous vertebrate genes and codon usage clock. Journal of Molecular Evolution 32, 6–15.CrossRefGoogle ScholarPubMed
Mevelec, M., Chardes, T., Mercereau-Piujalon, O., Bourguin, I., Archbarou, A., Dubremetz, J. & Bout, D. (1992). Molecular cloning of GRA4, a Toxoplasma gondii dense granule protein, recognised by mucosal IgA antibodies. Molecular and Biochemical Parasitology 56, 227–38.CrossRefGoogle ScholarPubMed
Muto, A. & Osawa, S. (1987). The G+C content of genomic DNA and bacterial evolution. Proceedings of the National Academy of Scienes, USA 84, 166–9.CrossRefGoogle Scholar
Nene, V., Iams, K. P., Gobright, E. I. & Musoke, A. J. (1992). Characterisation of the gene encoding a candidate vaccine antigen of Theileria parva sporozoites. Molecular and Biochemical Parasitology 51, 17–28.CrossRefGoogle ScholarPubMed
Ole-Mol Yoi, O. K., Sugimoto, C., Conrad, P. A. & Macklin, M. D. (1992). Cloning and characterisation of the casein kinase II alpha subunit gene from the lymphocyte-transforming intracellular protozoan parasite Theileria parva. Biochemistry 31, 6193–202.CrossRefGoogle Scholar
Osawa, S., Jukes, T. H., Watanabe, K. & Muto, A. (1992). Recent evidence for evolution of the genetic code. Microbiology Reviews 56, 229–64.CrossRefGoogle ScholarPubMed
Saul, A. & Battistutta, D. (1988). Codon usage in Plasmodium falciparum. Molecular and Biochemical Parasitology 27, 35–42.CrossRefGoogle ScholarPubMed
Sharp, P. M. & Devine, K. M. (1989). Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do ‘prefer’ optimal codons. Nucleic Acids Research 17, 5029–39.CrossRefGoogle ScholarPubMed
Sueoka, N. (1988). Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences, USA 85, 2653–7.CrossRefGoogle ScholarPubMed
Weber, J. L. (1987). Analysis of sequences from the extremely A + T-rich genome of Plasmodium falciparum. Gene 52, 103–9.CrossRefGoogle ScholarPubMed
Wright, F. (1990). The effective number of codons used in a gene. Gene 87, 23–9.CrossRefGoogle ScholarPubMed