Codon bias as a factor in regulating expression via translation rate in the human genome

Gene

Volumn 345, Issue 1 SPEC. ISS., 2005, Pages 127-138

  Lavner, Yizhar ^a   Kotlar, Daniel ^a  

^a TEL HAI COLLEGE   (Israel)

Author keywords

Biosynthetic cost; Codon bias; Gene expression; Homo sapiens; Optimal codon; Translation efficiency

Indexed keywords

AMINO ACID; DINUCLEOTIDE; NUCLEOTIDE; TRANSFER RNA;

AMINO ACID COMPOSITION; ARTICLE; CODON; COMPARATIVE STUDY; CORRELATION ANALYSIS; EUKARYOTE; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE NUMBER; HUMAN GENOME; INTRON; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; RNA TRANSLATION; UNTRANSLATED REGION;

EID: 13444291526     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.11.035     Document Type: Article

References (41)

1. H. Akashi Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy Genetics 136 3 1994 927 935
2. H. Akashi Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA Genetics 139 1995 1076 1677
3. H. Akashi, and T. Gojobori Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis Proc. Natl. Acad. Sci. U. S. A. 99 6 2002 3695 3700
4. G. Bernardi The mosaic genome of warm-blooded vertebrates Science 228 4702 1985 953 958
5. J.M. Comeron Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence Genetics 167 2004 1293 1304
6. H. Dong, L. Nilsson, and C.G. Kurland Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates J. Mol. Biol. 260 1996 649 663
7. M.J. Dufton Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins? J. Theor. Biol. 187 1997 165 173
8. L. Duret tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes Trends Genet. 16 7 2000 287 289
9. L. Duret Evolution of synonymous codon usage in metazoans Curr. Opin. Genet. Dev. 12 2002 640 649
10. L. Duret, and D. Mouchiroud Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis Proc. Natl. Acad. Sci. U. S. A. 96 8 1999 4482 4487
11. W. Fiers, and H. Grosjean On codon usage Nature 277 5694 1979 328
12. R. Grantham, C. Gautier, M. Gouy, R. Mercier, and A. Pave Codon catalog usage and the genome hypothesis Nucleic Acids Res. 8 1980 r49 r62
13. D. Graur, and W.-H. Li Fundamentals of molecular evolution 2nd ed. 2000 Mass Sinauer, Sunderland
14. J. Hey, and R.M. Kliman Interactions between natural selection, recombination and gene density in the genes of Drosophila Genetics 160 2002 595 608
15. T. Ikemura 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 1981 1 21
16. T. Ikemura Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs J. Mol. Biol. 158 4 1982 573 597
17. S. Kanaya, Y. Yamada, Y. Kudo, and T. Ikemura Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis Gene 238 1999 143 155
18. S. Kanaya, Y. Yamada, M. Kinouchi, Y. Kudo, and T. Ikemura Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis J. Mol. Evol. 53 2001 290 298
19. S. Karlin, and J. Mrazek What drives codon choices in human genes? J. Mol. Biol. 262 1996 459 472
20. S. Karlin, J. Mrazek, and A.M. Campbell Codon usages in different gene classes of the Escherichia coli genome Mol. Microbiol. 29 6 1998 1341 1355
21. R.D. Knight, S.J. Freeland, and L.F. Landweber A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes Genome Biol. 2 4 2001 (http://www. genomebiology.com/2001/2/4/research/010.1)
22. W. Konigsberg, and N. Godson Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli Proc. Natl. Acad. Sci. U. S. A. 80 3 1983 687 691
23. M. Kreitman, and J.M. Comeron Coding sequence evolution Curr. Opin. Genet. Dev. 9 6 1999 637 641
24. E.S. Lander International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature 409 2001 860 921
25. G. Marais, D. Mouchiroud, and L. Duret Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes Proc. Natl. Acad. Sci. U. S. A. 98 10 2001 5688 5692
26. Moriyama, E.N., 2003. Codon usage, Encyclopedia of the human genome. Macmillan Publishers, Nature Publishing Group. http://www.ehgonline.net.
27. E.N. Moriyama, and J.R. Powel Codon usage bias and tRNA abundance in Drosophila J. Mol. Evol. 45 1997 514 523
28. J.A. Novembre Accounting for background nucleotide composition when measuring codon usage bias Mol. Biol. Evol. 19 8 2002 1390 1394
29. S. Pedersen Escherichia coli ribosomes translate in vivo with variable rate EMBO J. 3 12 1984 2895 2898
30. R. Percudani, A. Pavesi, and S. Ottonello Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae J. Mol. Biol. 268 1997 322 330
31. M. Robinson Codon usage can affect efficiency of translation of genes in Escherichia coli Nucleic Acids Res. 12 17 1984 6663 6671
32. M.J. Saier Differential codon usage: a safe guard against inappropriate gene expression of specialized genes FEBS 362 1995 1 4
33. P.M. Sharp, and W.-H. Li Codon usage in regulatory genes in Escherichia coli does not reflect selection for rare codons Nucleic Acids Res. 14 1986 7737 7749
34. P.M. Sharp, T.M. Tuohy, and K.R. Mosurski Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes Nucleic Acids Res. 14 1986 5125 5143
35. A.O. Urrutia, and L.D. Hurst Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection Genetics 159 2001 1191 1199
36. A.O. Urrutia, and L.D. Hurst The signature of selection mediated by expression on human genes Genome Res. 13 10 2003 2260 2264
37. R. Versteeg The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes Genome Res. 13 9 2003 1998 2004
38. K.D. Wells, J.A. Foster, K. Moore, V.G. Pursel, and R.J. Wall Codon optimization, genetic insulation, and an rtTA reporter improve performance of the tetracycline switch Transgenic Res. 8 5 1997 371 381
39. F. Wright The 'effective number of codons' used in a gene Gene 87 1990 23 29
40. S. Zhang, G. Zubay, and E. Goldman Low usage codons in Escherichia coli, yeast, fruit fly, and primates Gene 105 1991 61 72
41. J. Zhou, W-J. Liu, S.W. Peng, X.Y. Sun, and I. Frazer Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability J. Virol. 73 1999 4972 4982