Synonymous codon usage is subject to selection in thermophilic bacteria

Nucleic Acids Research

Volumn 30, Issue 19, 2002, Pages 4272-4277

  Lynn, David J ^a   Singer, Gregory A C ^a   Hickey, Donal A ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

BACTERIAL GENOME; BACTERIAL GROWTH; CODON USAGE; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; GENE SEQUENCE; GENE TRANSFER; HIGH TEMPERATURE; NATURAL SELECTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; THERMOPHILIC BACTERIUM;

BACTERIA; BASE COMPOSITION; CODON; GENOME, BACTERIAL; PHYLOGENY; SELECTION (GENETICS); TEMPERATURE;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 0036796799     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (22)

1. Grantham,R., Gautier,C. and Gouy,C. (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res., 8, 1893-1912.
2. Ikemura,T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol., 146, 1.
3. Ikemura,T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol., 151, 389-409.
4. Ikemura, T. (1982) Differences in synonymous codon choice patterns of yeast and correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codons choice patterns of yeast. J. Mol. Biol., 158, 573-597.
5. Shields,D.C. and Sharp,P.M. (1987). Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res., 15, 8023-8040.
6. Shields,D.C., Sharp,P.M., Higgins,D.G. and Wright,F. (1988) "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol., 5, 704-716.
7. Stenico,M., Lloyd,A.T. and Sharp,P.M. (1994) Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res., 22, 2437-2446.
8. McInerney,J.O. (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA, 95, 10698-10703.
9. Bulmer,M. (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics, 129, 897-907.
10. Sharp,P.M. and Li,W.-H. (1987) The selection-mutation-drift theory of synonymous codon usage. Nucleic Acids Res., 15, 1281-1295.
11. Greenacre,M.J. (1984) Theory and Applications of Correspondence. Analysis. Academic Press, London, UK.
12. Gouy,M. and Gautier,C. (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res., 10, 7055-7074.
13. Xia,X. (1998) How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae? Genetics, 149, 37-44.
14. Aravind,L., Tatusov,R.L., Wolf,Y.I., Walker,D.R. and Koonin,E.V. (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet., 14, 442-444.
15. Nelson,K.E., Clayton,R.A., Gill,S.R., Gwinn,M.L. Dodson,R.J., Haft,D.H., Hickey,E.K., Peterson,J.D., Nelson,W.C., Ketchum,K.A. et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature, 399, 323-329.
16. Kanaya,S., Kinouchi,M., Abe,T., Kudo,Y., Yamada,Y., Nishi,T., Mori,H. and Ikemura,T. (2001) Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene, 276, 89-99.
17. Wang,H.C., Badger,J., Kearney,P. and Li,M. (2001) Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Mol. Biol. Evol., 18, 792-800.
18. Ochman,H., Lawrence,J.G. and Groisman,E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304.
19. Clarke,G.D., Beiko,R.G., Ragan,M.A. and Charlebois,R.L. (2002) Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol., 184, 2072-2080.
20. House,C.H. and Fitz-Gibbon,S.T. (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J. Mol. Evol., 54, 539-547.
21. Lao,P.J. and Forsdyke,D.R. (2000) Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res., 10, 228-236.
22. Kreil,D.P. and Ouzounis,C.A. (2001) Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res., 29, 1608-1615.