Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages

Biochemical and Biophysical Research Communications

Volumn 306, Issue 1, 2003, Pages 310-317

  Chen, Ling Ling ^a,b   Zhang, Chun Ting ^a  

^a TIANJIN UNIVERSITY   (China)

^b SHANDONG UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Codon usage; GC content; Microbial genomes; Phylogenetic lineage

Indexed keywords

ALGORITHM; ARTICLE; BUCHNERA; CAULOBACTER CRESCENTUS; CODON; CONTROLLED STUDY; DEINOCOCCUS RADIODURANS; GC RICH SEQUENCE; GENE FUNCTION; GENETIC ANALYSIS; GENOME; HAEMOPHILUS INFLUENZAE; HALOBACTERIUM; MICROBIAL GENETICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; SINORHIZOBIUM MELILOTI; VIBRIO CHOLERAE;

PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 0037716514     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(03)00973-2     Document Type: Article

References (20)

1. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
2. Muto A., Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA. 84:1987;166-169.
3. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:1985;13-34.
4. Trifonov E.N. Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. J. Mol. Biol. 194:1987;643-652.
5. Sharp P.M., Devine K.M. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Res. 17:1989;5029-5039.
6. Anderson S.G.E., Kurland C.G. Codon preferences in free-living micro organisms. Microbiol. Rev. 54:1990;198-210.
7. Wright F., Bibb M.J. Codon usage in the G. + C-rich Streptomyces genome Gene. 113:1992;55-65.
8. Zhang C.-T., Chou K.C. A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences. J. Mol. Biol. 238:1994;1-8.
9. Gutierrez G., Marquez L., Marin A. Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency. Nucleic Acids Res. 24:1996;2525-2527.
10. Wang J. The base contents of A, C, G or U for the three codon positions and the total coding sequences show positive correlation. J. Biomol. Struct. Dyn. 16:1998;51-57.
11. Pan A., Dutta C., Das J. Codon usage in highly expressed genes of Haemophilus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. Gene. 215:1998;405-413.
12. Frank A.C., Lobry J.R. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene. 238:1999;65-77.
13. Siemion I.Z., Siemion P.J. The informational context of the third base in amino acid codons. Biosystems. 33:1994;39-48.
14. Taylor F.J., Coates D. The code within the codons. Biosystems. 22:1989;177-187.
15. Salzberg S.L., Delcher A.L., Kasif S., White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:1998;544-548.
16. Borodovsky M., Mclninch J. GenMark: parallel gene recognition for both DNA strands. Comput. Chem. 17:1993;123-133.
17. Zhang C.-T., Zhang R. Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res. 19:1991;6313-6317.
18. Zhang R., Zhang C.-T. Z curves, an intuitive tool for visualizing the DNA sequences. J. Biomol. Struct. Dyn. 11:1994;767-782.
19. Guo F.B., Ou H.Y., Zhang C.-T. ZCURVE: a new system for recognizing protein coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 31:2003;1780-1789.
20. Dillon W.R., Goldstein M. Multivariate Analysis, Methods and Applications. 1984;Wiley, New York, USA.