Comparative codon and amino acid composition analysis of Tritryps-conspicuous features of Leishmania major

FEBS Letters

Volumn 581, Issue 30, 2007, Pages 5751-5758

  Chanda, Ipsita ^a   Pan, Archana ^b   Saha, Sanjoy Kumar ^a   Dutta, Chitra ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

^b DEPARTMENT OF MATERIALS SCIENCE   (India)

Author keywords

Aromaticity; Correspondence analysis; GC bias; Gene expressivity; Hydropathy; Principle of cost minimization

Indexed keywords

AMINO ACID;

ARTICLE; CODON; CONTROLLED STUDY; COST MINIMIZATION ANALYSIS; GAS CHROMATOGRAPHY; GENE EXPRESSION; GENETIC VARIABILITY; LEISHMANIA MAJOR; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTOZOON; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO ACIDS; ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CODON; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; GENES, PROTOZOAN; LEISHMANIA MAJOR; MEMBRANE GLYCOPROTEINS; MOLECULAR SEQUENCE DATA; PARASITES; PROTOZOAN PROTEINS; TRYPANOSOMA BRUCEI BRUCEI; TRYPANOSOMA CRUZI; VARIATION (GENETICS);

LEISHMANIA MAJOR; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

EID: 36849050693     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.11.041     Document Type: Article

References (23)

1. El-Sayed N.M., Myler P.J., Blandin G., et al. Comparative genomics of trypanosomatid parasitic protozoa. Science 309 (2005) 404-409
2. Parsons M., Worthey E.A., Ward P.N., and Mottram J.C. Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi. BMC Genomics 6 (2005) 127-145
3. El-Sayed N.M., Myler P.J., Bartholomeu D.C., et al. The genome sequence of Trypanosoma cruzi, etiologic agent of chagas disease. Science 309 (2005) 409-415
4. Berriman M., Ghedin E., Hertz-Fowler C., et al. The genome of the African trypanosome Trypanosoma brucei. Science 309 (2005) 416-422
5. Ivens A.C., Peacock C.S., Worthey E.A., et al. The genome of the kinetoplastid parasite, Leishmania major. Science 309 (2005) 436-442
6. Borst P., and Ouellette M. New mechanisms of drug resistance in parasitic protozoa. Annu. Rev. Microbiol. 49 (1995) 427-460
7. Musto H., Rodríguez-Maseda H., and Bernardi G. The nuclear genomes of African and American trypanosomes are strikingly different. Gene 141 (1994) 63-69
8. NecÅŸulea A., and Lobry J.R. Revisiting the directional mutation pressure theory: the analysis of a particular genomic structure in Leishmania major. Gene 385 (2006) 28-40
9. Sharp P.M., and Li W.H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
10. Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
11. Lobry J.R., and Gautier C. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 22 (1994) 3174-3180
12. Das S., Ghosh S., Pan A., and Dutta C. Compositional variation in bacterial genes and proteins with potential expression level. FEBS Lett. 579 (2005) 5205-5252
13. Greenacre M. Theory and Application of Correspondence Analysis (1984), Academic, London
14. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
15. Sueoka N. Directional mutation pressure, selective constraints ad genetic equilibria. J. Mol. Evol. 34 (1992) 95-114
16. Machado C.R., Augusto-Pinto L., McCulloch R., and Teixeira S.M. DNA metabolism and genetic diversity in Trypanosomes. Mutat. Res. 612 (2006) 40-57
17. Dubois M.E., Demick K.P., and Mansfield J.M. Trypanosomes expressing a mosaic variant surface glycoprotein coat escape early detection by the immune system. Infect. Immun. 73 (2005) 2690-2697
18. Buscaglia C.A., Campo V.A., Di Noia J.M., Torrecilhas A.C., De Marchi C.R., Ferguson M.A., Frasch A.C., and Almeida I.C. The surface coat of the mammal-dwelling infective trypomastigote stage of Trypanosoma cruzi is formed by highly diverse immunogenic mucins. J. Biol. Chem. 279 (2004) 15860-15869
19. Seligmann H. Cost-minimization of amino acid usage. J. Mol. Evol. 56 (2003) 151-161
20. Chanda I., Pan A., and Dutta C. Proteome composition in Plasmodium falciparum: higher usage of GC-rich nonsynonymous codons in highly expressed genes. J. Mol. Evol. 61 (2005) 513-523
21. Sharp P.M., and Li W.H. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 4 (1987) 222-230
22. Alvarez F., Robello C., and Vignali M. Evolution of codon usage and base contents in kinetoplastid protozoans. Mol. Biol. Evol. 11 (1994) 790-802
23. Stevens J.R., Noyes H.A., Dover G.A., and Gibson W.C. The ancient and divergent origins of the human pathogenic trypanosomes, Trypanosoma brucei and T. cruzi. Parasitology 118 (1999) 107-116