Factors affecting codon usage in Yersinia pestis

Acta Biochimica et Biophysica Sinica

Volumn 35, Issue 6, 2003, Pages 580-586

  Hou, Zhuo Cheng ^a   Yang, Ning ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Coding sequence length; Codon usage; Correspondence analysis; Gene expression level; Yersinia pestis

Indexed keywords

ADENINE; CYTOSINE; GUANINE; THYMINE;

ARTICLE; BACTERIAL GENOME; BASE PAIRING; CODON USAGE; GENE EXPRESSION REGULATION; GENE LOCATION; GENE REPLICATION; GENETIC ANALYSIS; GENETIC CODE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; SPECIES COMPARISON; YERSINIA PESTIS;

AMINO ACIDS; BASE COMPOSITION; CODON; DNA REPLICATION; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; TRANSCRIPTION, GENETIC; YERSINIA PESTIS;

BACTERIA (MICROORGANISMS); YERSINIA; YERSINIA PESTIS;

EID: 0042386315     PISSN: 05829879     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (25)

1. Wada K, Aota S, Tsuchiya R, Ishibashi F, Gojobori T, Ikemura T. Codon usage tabulated from the GeneBank genetic sequence data. Nucleic Acids Res, 1990, 18(Suppl):2367-2411
2. Bennetzen JL, Hall BD. Codon selection in yeast. J Biol Chem, 1982, 257:3026-3031
3. Sueoka K, Kawanishi Y. DNA G + C content of the third codon position and codon usage biases of human genes. Gene, 2000, 261: 53-62
4. Hou ZC, Yang N. Analysis of factors shaping S.penumoniae codon usage. Acta Genetica Sinica, 2002, 29(8):747-752
5. Kerr AR, Peden JF, Sharp PM. Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae. Mol Microbiol, 1997, 25:1177-1179
6. Naya H, Romero H, Carels N, Zavala A, Musto H. Translational selection shapes codon usage in the GC-rich genomes of Chlamydomonas reinhardtii. FEBS Lett, 2001, 501:127-130
7. Romero H, Zavala A, Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res, 2000, 28: 2084-2090
8. Parkhill J, Wern BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M et al. Genome sequence of Yersinia pesits, the causative agent of plague. Nature, 2001, 413:523-527
9. Sharp PM, Tuohy TM, Mosurski KR. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res, 1986, 14:5125-5143
10. Wright F. The 'effective number of codons' used in a gene. Gene, 1990, 87:23-29
11. Sharp PM, Li WH. The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res, 1987, 15:1281-1295
12. Gupta SK, Ghosh TC. Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene, 2001, 273:63-70
13. Bellgard M, Schibeci D, Trifonov E, Gojobori T. Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J Mol Evol, 2001, 53(4-5):465-468
14. Jenkins GM, Pagel M, Gould EA, de A Zanotto PM, Holmes EC. Evolution of base composition and codon usage bias in the genus Flasvivirus. J Mol Evol, 2001, 52:383-390
15. Moriyama EN, Powell JR. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res, 1998, 26:3188-3193
16. Powell JR, Moriyama EN. Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA, 1997, 94:7784-7790
17. Romero H, Zavala A, Musto H. Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica. Gene, 2000, 242: 307-311
18. Comeron JM, Kreitman M, Aguade M. Natural selection on synonymous sites correlates with gene length and recombination in Drosophila. Genetics, 1999, 151: 239-249
19. McInerney JO. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA, 1998, 95: 10698-10703
20. Lobry JR. Origin of replication of Mycoplasma genitalium. Science, 1996, 272:745-746
21. Blattner FR, Plunkett GM, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J et al. The complete genome sequence of Escherichia coli K-12. Science, 1997, 277:1453-1474
22. Fernandez V, Zavala A, Musto H. Evidence for translational selection in codon usage in Echinococcus spp. Parasitology, 2001, 123 (Pt2): 203-209
23. Kliman RM, Hey J. The effects of mutation and natural selections on codon bias in the genes of Drosophila. Genetics, 1994, 137(4):1049-1056
24. Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis. Drosophila, and Arabidopsis. Proc Natl Acad Sci USA, 1999, 96:4482-4487
25. Coghlan A, Wolfe KH. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast, 2000, 16:1131-1145