Studies on codon usage in Entamoeba histolytica

International Journal for Parasitology

Volumn 30, Issue 6, 2000, Pages 715-722

  Ghosh, T C ^a   Gupta, S K ^a   Majumdar, S ^a  

^a BOSE INSTITUTE   (India)

Author keywords

Codon usage; Compositional constraints; Correspondence analysis; Effective number of codons; Entamoeba histolytica; Highly expressed genes; Lowly expressed genes; Multivariate statistical analysis; Mutational bias; Parasite; Translational selection

Indexed keywords

GENE PRODUCT;

ARTICLE; CODON USAGE; DNA SEQUENCE; ENTAMOEBA HISTOLYTICA; GENE EXPRESSION; GENOME; MUTATION; NONHUMAN;

ANIMALS; CODON; DNA MUTATIONAL ANALYSIS; DNA, PROTOZOAN; ENTAMOEBA HISTOLYTICA; GENE LIBRARY; MOLECULAR SEQUENCE DATA; STRUCTURE-ACTIVITY RELATIONSHIP; VARIATION (GENETICS);

ENTAMOEBA HISTOLYTICA; PROTOZOA;

EID: 0034193767     PISSN: 00207519     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0020-7519(00)00042-4     Document Type: Article

References (33)

1. Martin A., Bertranpetit J., Oliver J.L., Medina J.R. Variation in G+C content and codon choice: differences among synonymous codon groups in vertebrate genes. Nucl. Acids Res. 17:1989;6181-6189.
2. Lloyd A.T., Sharp P.M. Evolution of codon usage patterns: The extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucl. Acids Res. 20:1992;5289-5295.
3. Moriyama E.N., Hartl D.L. Codon usage bias and base composition of nuclear genes in Drosophila. Genetics. 134:1993;847-858.
4. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucl. Acids Res. 10:1982;5303-5318.
5. Grantham R., Gautier C., Gouy M., Jacobzone M., Mercier R. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucl. Acids Res. 9:1981;r43-r74.
6. Ohkubo S., Muto A., Kawauchi Y., Yamao F., Osawa S. The ribosomal protein gene cluster of Mycoplasma capricolum. Mol. Gen. Genet. 210:1987;314-322.
7. Wright F., Bibb M.J. Codon usage in the G+C rich Streptomyces genome. Gene. 113:1992;55-65.
8. Musto H., Romero H., Maseda H.R. Heterogeneity in codon usage in the flatworm Schistosoma mansoni. J. Mol. Evol. 46:1998;159-167.
9. Bernardi G. The human genome: Organization and evolutionary history. Ann. Rev. Genet. 29:1995;445-476.
10. Aota S., Ikemura T. Diversity in G+C content at the third position of codons in vertebrate genes and its cause. Nucl. Acids Res. 14:1986;6345-6355.
11. Bernardi G., Olofsson B., Filipski J., et al. The moasic genome of warm-blooded vertebrates. Science. 228:1985;953-956.
12. Musto H., Romero H., Zavala A., Bernardi G. Compositional correlations in the chicken genome. J. Mol. Evol. 49:1999;325-329.
13. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151:1981;389-409.
14. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucl. Acids Res. 10:1982;7055-7074.
15. Shields D., Sharp P. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational constraints. Nucl. Acids Res. 15:1987;8023-8040.
16. Anderson S.G.E., Sharp P.M. Codon usage in the Mycobacterium tuberculosis complex. Microbiology. 142:1996;915-925.
17. Sharp P., Tuohy T., Mosurski K. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucl. Acids Res. 14:1986;5125-5143.
18. Chiapello H., Ollivier E., Landes-Devauchelle C., Nitschke P., Risler J.-L. Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucl. Acids Res. 27:1999;2848-2851.
19. McInerney J.O. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA. 95:1998;10698-10703.
20. Li E., Stanley S.L. Jr. Protozoa. Amebiasis. Gastroenterol. Clin. North Am. 25:1996;471-492.
21. Carrero J.C., Laclette J.P. Molecular biology of Entamoeba histolytica: a review. Arch. Med. Res. 27:1996;403-412.
22. Horstmann R.D., Leippe M., Tannich E. Recent progress in the molecular biology of Entamoeba histolytica. Trop. Med. Parasitol. 43:1992;213-218.
23. Char S., Farthing M.J. Codon usage in Entamoeba histolytica. Int. J. Parasitol. 22:1992;381-383.
24. Bhattacharya A, Satish S, Bagchi A, Bhattacharya S. The genome of Entamoeba histolytica. Int J Parasitol 2000; 30:401-10.
25. McInerney J.O. GCUA: General codon usage analysis. Bioinformatics. 14:1998;372-373.
26. Wright F. The 'effective number of codons' used in a gene. Gene. 87:1990;23-29.
27. Sharp P.M., Li W.-H. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucl. Acids Res. 14:1986;7737-7749.
28. Greenacre M.J. Theory and applications of correspondence analysis. 1984;Academic Press, London.
29. Stenico M., Lloyd A.T., Sharp P.M. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucl. Acids Res. 22:1994;2437-2446.
30. Musto H., Romero H., Zavala A., Jabbari K., Bernardi G. Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: compositional constraints and translational selection. J. Mol. Evol. 49:1999;27-35.
31. Pan A., Dutta C., Das J. Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. Gene. 215:1998;405-413.
32. Shepherd J.C.W. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc. Natl. Acad. Sci. USA. 78:1981;1596-1600.
33. Gutierrez G., Marquez L., Marin A. Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency. Nucl. Acids Res. 24:1996;2525-2527.