Patterns of context-dependent codon biases

Biochemical and Biophysical Research Communications

Volumn 304, Issue 1, 2003, Pages 86-90

  Fuglsang, Anders ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Codon context; Codon usage; Contingency tables; Mutational pressure

Indexed keywords

BACTERIAL PROTEIN; PROTEIN SHC;

ARTICLE; BACTERIUM; CODON; CONTROLLED STUDY; ENCEPHALITOZOON CUNICULI; INTRON; NONHUMAN; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE;

BACTERIA (MICROORGANISMS); ENCEPHALITOZOON CUNICULI; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 0037466470     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(03)00530-8     Document Type: Article

References (26)

1. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:1982;7055-7074.
2. Duret L., Muchiroud D. Expression pattern and, surprisingly, gene length, shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. Sci. USA. 96:1999;4482-4487.
3. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the relative occurence of the respective codons in protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 21:1981;389-409.
4. Ikemura T. Codon usage and tRNA is unicellular and multicellular organisms. Mol. Biol. Evol. 2:1985;13-34.
5. 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.
6. Andersson G.E., Sharp P.M. Codon usage in the Mycobacterium tuberculosis complex. Microbiology. 142:1996;915-925.
7. Romero H., Zavala A., Musto H. Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica. Gene. 242:2000;307-311.
8. McLean M.J., Wolfe K.H., Devine K.M. Base compositional skews, replication origientation and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47:1998;691-696.
9. Lopez P., Phillipe H. Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation. Life Sci. 324:2001;201-208.
10. Lobry J.R., Sueoka N. Asymmetric directional mutation pressure in bacteria. Genome Biol. 3:2002;1-14.
11. Moriyama E.N., Powell J.R. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26:1998;3188-3193.
12. Oresic M., Shalloway D. Specific correlations between relative synonymous codon usage and protein secondary structure. J. Mol. Biol. 281:1998;31-48.
13. Tao X., Dafu D. The relationship between synonymous codon usage and protein structure. FEBS Lett. 434:1998;93-96.
14. Bulmer M. The effect of context on synonymous codon usage in genes with low codon usage bias. Nucleic Acids Res. 18:1990;2869-2873.
15. McVean G.A., Hurst G.D. Evolutionary lability of context-dependent codon bias in bacteria. J. Mol. Evol. 50:2000;264-275.
16. Miyasaka H. The positive relationship between codon usage bias and translation initiation AUG context in Saccharomyces cerevisiae. Yeast. 15:1999;633-637.
17. Miyasaka H. Translation initiation AUG context varies with codon usage bias and gene length in Drosophila melanogaster. J. Mol. Evol. 55:2002;52-64.
18. Morton B.R., So B.G. Codon usage in plastid genes is correlated with context, position within the gene, and amino acid content. J. Mol. Evol. 50:2000;184-193.
19. Fedorov A., Saxonov S., Gilbert W. Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 30:2002;1192-1197.
20. 2 -tests Biometrics. 10:1954;417-451.
21. Berg O.G., Silva P.J. Codon bias in Escherichia coli: the influence of codon context on mutation and selection. Nucleic Acids Res. 25:1997;1397-1404.
22. Looman A.C., Laude M., Stahl U. Influence of the codon following the initiation codon on the expression of the lacZ gene in Saccharomyces cerevisiae. Yeast. 7:1991;157-165.
23. Wuitschick J.D., Karrer K.M. Analysis of genomic G. + C content, codon usage, initiator codon context and translation termination sites in Tetrahymena thermophila J. Eukaryot. Microbiol. 46:1999;239-247.
24. Stenström C.M., Holmgren E., Isaksson L.A. Cooperative effects by the initiation codon and its flanking regions on translation initiation. Gene. 273:2001;259-265.
25. Etchegaray J.P., Inouye M. Translational enhancement by an element downstream of the initiation codon in Escherichia coli. J. Biol. Chem. 274:1999;10079-10085.
26. Etchegaray J.P., Inouye M. A sequence downstream of the initiation codon is essential for cold shock induction of cspB of Escherichia coli. J. Bacteriol. 181:1999;5852-5854.