Hostname: page-component-76fb5796d-qxdb6 Total loading time: 0 Render date: 2024-04-25T09:25:40.074Z Has data issue: false hasContentIssue false
  • English
  • Français

Schistosoma mansoni: patterns of codon usage and bias

Published online by Cambridge University Press:  06 April 2009

J. T. Ellis  and
D. A. Morrison
J. T. Ellis
Affiliation:
School of Biological and Biomedical Sciences, University of Technology Sydney, Westborne Street, Gore Hill, NSW 2065, Australia
D. A. Morrison
Affiliation:
School of Biological and Biomedical Sciences, University of Technology Sydney, Westborne Street, Gore Hill, NSW 2065, Australia
Get access Rights & Permissions [Opens in a new window]

Extract

Codon usage and bias has been examined in 20 genes of Schistosoma mansoni. Significant heterogeneity was detected in the patterns of codon usage and bias among genes by metric multidimensional scaling and three general indictors of bias (GC3S, Nc and B). In keeping with observations on sporozoan parasites, 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 over or under-represented in the sequences.

Keywords

Schistosoma mansonicodon usagebias
Type
Research Article
Information
Parasitology , Volume 110 , Issue 1 , January 1995 , pp. 53 - 60
Copyright
Copyright © Cambridge University Press 1995

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Andersson, S. G. E. & Kurland, C. G. (1990). Codon preferences in free-living micro-organisms. Microbiological Reviews 54, 198–210.CrossRefGoogle Scholar
Andresen, K., Tom, T. D. & Strand, M. (1991). Characterisation of cDNA clones encoding a novel calcium-activated neutral proteinase from Schistosoma mansoni. Journal of Biological Chemistry 266, 15085–90.CrossRefGoogle ScholarPubMed
Belbin, L. (1989). PATN-Pattern Analysis Package Technical Reference. CSIRO, Canberra.Google Scholar
Bernardi, G. & Bernardi, G. (1985). Codon usage and genome composition. Journal of Molecular Evolution 22, 363–5.CrossRefGoogle ScholarPubMed
Cao, M., Akridge, R., Weston, D., Kemp, W. M. & Doughty, B. L. (1992). Schistosoma mansoni: cloning and sequencing of a gene for adenylate kinase. Experimental Parasitology 74, 357–9.CrossRefGoogle ScholarPubMed
Craig, S. P., McKerrow, J. H., Newport, G. R. & Wang, C. C. (1988). Analysis of cDNA encoding the hypoxanthine–guanine phosphoribosyltransferase (HGPRTase) of Schistosoma mansoni: a putative target for chemotherapy. Nucleic Acids Research 16, 7087–101.CrossRefGoogle ScholarPubMed
Davis, A. H., Nanduri, J. & Watson, D. C. (1987). Cloning and gene expression of Schistosoma mansoni protease. Journal of Biological Chemistry 262, 12851–5.CrossRefGoogle ScholarPubMed
Devereux, J., Haeberli, P. & Smithies, O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12, 216–23.CrossRefGoogle ScholarPubMed
Dietzel, J., Hirzmann, J., Preis, D., Symmons, P. & Kunz, W. (1992). Ferritins of Schistosoma mansoni: sequence comparison and expression in female and male worms. Molecular and Biochemical Parasitology 50, 245–54.CrossRefGoogle ScholarPubMed
Duvaux-Miret, O., Blandine, B., Dissous, C. & Capron, A. (1991). Molecular cloning and sequencing of the alpha tubulin gene from Schistosoma mansoni. Molecular and Biochemical Parasitology 49, 337–40.CrossRefGoogle ScholarPubMed
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
Ellis, J., Morrison, D. A., Avery, D. & Johnson, A. M. (1994). Codon usage and bias among individual genes of the coccidia and piroplasms. Parasitology (in the Press).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
Francis, P. & Bickle, Q. (1992). Cloning of a 21·1 kDa vaccine-dominant antigen gene of Schistosoma mansoni reveals an EF hand-like motif. Molecular and Biochemical Parasitology 50, 215–24.CrossRefGoogle Scholar
Johnston, D. A., Dias, Neto E., Simpson, A. J. G. & Rollinson, D. (1993). Opening the can of worms: molecular analysis of schistosome populations. Parasitology Today 9, 286–91.CrossRefGoogle Scholar
Karcz, S. R., Podestr, R. B., Siddiqui, A. A., Dekaban, G. A., Strejan, G. H. & Clarke, M. W. (1991). Molecular cloning and sequence analysis of a calcium-activated neutral protease (calpain) from Schistosoma mansoni. Molecular and Biochemical Parasitology 49, 333–6.CrossRefGoogle ScholarPubMed
Klinkert, M. Q., Felleisen, R., Link, G., Ruppel, A. & Beck, E. (1989). Primary structures of Sm31/32 diagnostic proteins of Schistosoma mansoni and their identification as proteases. Molecular and Biochemical Parasitology 33, 113–22.CrossRefGoogle ScholarPubMed
Laclette, J. P., Landa, A., Arcos, L., Willms, K., Davis, A. E. & Shoemaker, c. B. (1991). Paramyosin is the Schistosoma mansoni (Trematoda) homologue of antigen B from Taenia solium (Cestoda). Molecular and Biochemical Parasitology 44, 287–95.CrossRefGoogle ScholarPubMed
Lloyd, A. T. & Sharp, P. M. (1992 a). 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
Lloyd, A. T. & Sharp, P. M. (1992 b). CODONS: A microcomputer program for codon usage analysis. Journal of Heredity 83, 239–40.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
Meadows, H. M. & Simpson, A. J. G. (1989). Codon usage in Schistosoma. Molecular and Biochemical Parasitology 36, 291–9.CrossRefGoogle ScholarPubMed
Mehlhorn, H. & Walldorf, V. (1988). Life cycles. Phylum Platyhelminthes. In: Parasitology in Focus (ed. Mehlhorn, H.), pp. 53–87. Berlin: Springer-Verlag.CrossRefGoogle Scholar
Neumann, S., Ziv, E., Lantner, F. & Schecter, I. (1992). Cloning and sequencing of an hsp70 gene of Schistosoma mansoni. Molecular and Biochemical Parasitology 56, 357–60.CrossRefGoogle ScholarPubMed
Newport, G., McKerrow, J. H., Hedstrom, R., Petitt, M., McGarrigle, L., Barr, P. J. & Agabian, N. (1988). Cloning of the proteinase that facilitates infection by schistosome parasites. Journal of Biological Chemistry 263, 13179–84.CrossRefGoogle ScholarPubMed
Osawa, S., Jukes, T. H., Watanabe, K. & Muto, A. (1992). Recent evidence for evolution of the genetic code. Microbiological Reviews 56, 229–64.CrossRefGoogle ScholarPubMed
Rajkowic, A., Simonsen, J. N., Davis, R. E. & Rottman, F.M. (1989). Molecular cloning and sequence analysis of 3-hydroxy-3-methylglutaryl-coenzyme A reductase from the human parasite Schistosoma mansoni. Proceedings of the National Academy of Sciences, USA 86, 8217–21.CrossRefGoogle Scholar
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
Sharp, P. M. & Lloyd, A. T. (1993). Regional base composition along yeast chromosome III: evolution of chromosome promary structure. Nucleic Acids Research 21, 179–183.CrossRefGoogle Scholar
Shoemaker, C. B., Ramachandran, H., Landa, A., Dos-Reis, M. G. & Stein, L. D. (1992 a). Alternative splicing of the Schistosoma mansoni gene encoding a homologue of epidermal growth factor receptor. Molecular and Biochemical Parasitology 53, 17–32.CrossRefGoogle ScholarPubMed
Shoemaker, C., Gross, A., Gebremichael, A. & Harn, D. (1992 b). cDNA cloning and functional expression of the Schistosoma mansoni protective antigen triosephosphate isomerase. Proceedings of the National Academy of Sciences, USA 89, 1842–6.CrossRefGoogle Scholar
Stein, L. D., Harn, D. A. & David, J. R. (1990). A cloned ATP: guanidino kinase in the trematode Schistosoma mansoni has a novel duplicated structure. Journal of Biological Chemistry 265, 6582–8.CrossRefGoogle Scholar
Wada, K., Aota, S., Tsuchiya, R., Ishibashi, F., Gojobori, T. & Ikemura, T. (1990). Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Research 18, 2367–8.CrossRefGoogle ScholarPubMed
Weston, D., Schmitz, J., Kemp, W. M. & Kunz, W. (1993). Cloning and sequencing of a complete myosin heavy chain cDNA from Schistosoma mansoni. Molecular and Biochemical Parasitology 58, 161–4.CrossRefGoogle ScholarPubMed
Williams, D. L., Pierce, R. J., Cookson, E. & Capron, A. (1991). Molecular cloning and sequencing of glutathione peroxidase from Schistosoma mansoni. Molecular and Biochemical Parasitology 52, 127–30.CrossRefGoogle Scholar
World Health Organization (1985). The control of schistosomiasis. Report of a WHO Expert Committee, Geneva. WHO, Technical Report Series, No. 728.Google Scholar
World Health Organization (1990). Health Education in the Control of Schistosomiasis. Geneva: World Health Organization.Google Scholar
Wright, F. (1990). The effective number of codons used in a gene. Gene 87, 23–9.CrossRefGoogle ScholarPubMed
Wright, M., Henkle, K. & Mitchell, G. (1990). An immunogenic Mr 23000 integral membrane protein of Schistosoma mansoni worms that closely resembles a human tumour-associated signal. Journal of Immunology 144, 3195–200.CrossRefGoogle Scholar