Strand-specific mutational bias influences codon usage of weakly expressed genes in Escherichia coli

Genes to Cells

Volumn 15, Issue 7, 2010, Pages 773-782

  Powdel, Bhesh Raj ^a   Borah, Munindra ^a   Ray, Suvendra K ^a  

^a TEZPUR UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; CODON USAGE; DNA STRAND; ESCHERICHIA COLI; GENE EXPRESSION; GENE MUTATION; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

CODON; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MUTAGENESIS; MUTATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 77954157176     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/j.1365-2443.2010.01417.x     Document Type: Article

References (52)

1. Arakawa K, Tomita M. Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes. Evol. Bioinform. 2007, 3:279-286.
2. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. The Mosaic genome of warm-blooded vertebrates. Science 1985, 228:953-958.
3. Bremer H, Dennis PP. Modulation of chemical composition and other parameters of the cell by growth rate. Escherichia coli and Salmonella: Cellular and Molecular Biology 1996, 1553-1569. Neidhardt F, eds, and others), Washington DC, American Society for Microbiology
4. Bulmer M. Coevolution of codon usage and transfer RNA abundance. Nature 1987, 325:728-730.
5. Bulmer M. Are codon usage patterns in unicellular organisms determined by a mutation-selection balance? J. Evol. Biol. 1988, 1:15-26.
6. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 1991, 129:897-907.
7. Chen SL, Lee W, Hotts AK, Shapiro L, McAdams HH. Codon usage between genomes is constrained by genome wide mutational processes. Proc. Natl Acad. Sci. USA 2004, 101:3480-3485.
8. Daubin V, Perrière G. G+C structuring along the genome: a common feature in prokaryotes. Mol. Biol. Evol. 2003, 20:471-483.
9. Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 2000, 16:287.
10. 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.
11. Eyre-Walker A, Bulmer M. Synonymous substitution rates in enterobacteria. Genetics 1995, 140:1407-1412.
12. Francino MP, Ochman H. Strand asymmetries in DNA evolution. Trends Genet. 1997, 13:240-245.
13. Francino MP, Ochman H. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 2001, 18:1147-1150.
14. Frank AC, Lobry JR. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 1999, 238:65-77.
15. Freeman JM, Plasterer TN, Smith TF, Mohr SC. Patterns of genome organization in bacteria. Science 1998, 279:1827a.
16. Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982, 10:7055-7074.
17. Grantham R, Gautier C, Gouy M, Mercier R, Pavé A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980, 8:r49-r62.
18. Grosjean H, Fiers W. Preferential codon usage in prokaryotic genes: optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 1982, 18:199-209.
19. Hershberg R, Petrov DA. Selection on codon bias. Annu. Rev. Genet. 2008, 42:287-299.
20. Hinds PW, Blake RD. Delineation of coding areas in DNA sequences through assignment of codon probabilities. J. Biomol. Struct. Dyn. 1985, 3:543-549.
21. Hu J, Zhao X, Yu J. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Genomics 2007, 90:186-194.
22. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol. 1981, 151:389-409.
23. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 1985, 2:13-34.
24. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 2008, 9:102.
25. Konigsberg WJN, Godson GN. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc. Natl Acad. Sci. USA 1983, 80:687-691.
26. Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 1996, 13:660-665.
27. Lobry JR, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol. 2002, 3:0058.1-0058.14. Research
28. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genome sequences. Nucleic Acids Res. 1997, 25:955-964.
29. Mackiewicz P, Gierlik A, Kowalczuk M, Dudek MR, Cebrat S. How does replication-associated mutational pressure influence amino acid composition of proteins? Genome Res. 1999, 9:409-416.
30. McInerney JO. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl Acad. Sci. USA 1998, 95:10698-10703.
31. Mclean MJ, Wolfe KH, Devine KM. Base composition skews, replication orientation and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 1998, 47:691-696.
32. Morton RA, Morton BR. Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes. BMC Genomics 2007, 8:368.
33. Muto A, Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl Acad. Sci. USA 1987, 84:166-169.
34. Ochman H. Neutral mutations and neutral substitutions in bacterial genomes. Mol. Biol. Evol. 2003, 20:2091-2096.
35. Osawa S, Jukes TH, Watanabe K, Muto A. Recent evidence for evolution of the genetic code. Microbiol. Rev. 1992, 56:229-264.
36. Peden JF. CodonW 1999, PhD Thesis, University of Nottingham
37. Rocha EPC. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 2004, 14:2279-2286.
38. Rocha EPC, Danchin A, Viari A. Universal replication biases in bacteria. Mol. Microbiol. 1999, 32:11-16.
39. Rocha EPC, Touchon M, Feil EJ. Similar compositional biases are caused by very different mutational effects. Genome Res. 2006, 16:1537-1547.
40. Satapathy SS, Dutta M, Ray SK. Variable correlation of genome GC% with transfer RNA number as well as with transfer RNA diversity among bacterial groups: α-Proteobacteria and Tenericutes exhibit strong positive correlation. Microbiol. Res. 2010, 165:232-242.
41. Se′mon M, Lobry JR, Duret L. No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol. Biol. Evol. 2006, 23:523-529.
42. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 2005, 33:1141-1153.
43. Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 1986a, 24:28-38.
44. Sharp PM, Li WH. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 1986b, 14:7737-7749.
45. Sharp PM, Li WH. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 1987a, 4:222-230.
46. Sharp PM, Li WH. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987b, 15:1281-1295.
47. 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.
48. Sueoka N. On the genetic basis of variation and hetero-geneity of DNA base composition. Proc. Natl Acad. Sci. USA 1962, 48:582-591.
49. Sueoka N. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 1999, 238:53-58.
50. Touchon M, Hoede C, Tenaillon O. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009, 5:e1000344.
51. Walker JE, Saraste M, Gay NJ. The unc operon, nucleotide sequence, regulation and structure of ATP-synthase. Biochim. Biophys. Acta 1984, 768:164-200.
52. Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW. Origin of replication in circular prokaryotic chromosomes. Environ. Microbiol. 2006, 8:353-361.