Positive selection for unpreferred codon usage in eukaryotic genomes

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Neafsey, Daniel E ^a   Galagan, James E ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CODON USAGE; CONTROLLED STUDY; CRYPTOCOCCUS; DROSOPHILA; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOME; MUTATION RATE; NONHUMAN; OPEN READING FRAME; SACCHAROMYCES; ANIMAL; CODON; EUKARYOTIC CELL; FUNGAL GENE; GENE; GENETIC SELECTION; GENETICS;

EUKARYOTA; SACCHAROMYCES;

ANIMALS; CODON; CRYPTOCOCCUS; DROSOPHILA; EUKARYOTIC CELLS; GENES, FUNGAL; GENES, INSECT; OPEN READING FRAMES; SACCHAROMYCES; SELECTION (GENETICS);

EID: 34547657193     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-119     Document Type: Article

References (54)

1. Codon catalog usage is a genome strategy modulated for gene expressivity. R Grantham C Gautier M Gouy M Jacobzone R Mercier, Nucleic Acids Res 1981 9 1 r43 74 7208352 10.1093/nar/9.1.213-b
2. Gene expression and molecular evolution. H Akashi, Curr Opin Genet Dev 2001 11 6 660 666 10.1016/S0959-437X(00)00250-1 11682310
3. Evolution of synonymous codon usage in metazoans. L Duret, Curr Opin Genet Dev 2002 12 6 640 649 10.1016/S0959-437X(02)00353-2 12433576
4. Hearing silence: non-neutral evolution at synonymous sites in mammals. JV Chamary JL Parmley LD Hurst, Nat Rev Genet 2006 7 2 98 108 10.1038/nrg1770 16418745
5. Codon usage and tRNA content in unicellular and multicellular organisms. T Ikemura, Mol Biol Evol 1985 2 1 13 34 3916708
6. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. H Akashi, Genetics 1994 136 3 927 935 8005445
7. Codon usage can affect efficiency of translation of genes in Escherichia coli. M Robinson R Lilley S Little JS Emtage G Yarranton P Stephens A Millican M Eaton G Humphreys, Nucleic Acids Res 1984 12 17 6663 6671 6091031 10.1093/nar/12.17.6663
8. In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. DB Carlini W Stephan, Genetics 2003 163 1 239 243 12586711
9. Codon preferences in free-living microorganisms. SG Andersson CG Kurland, Microbiol Rev 1990 54 2 198 210 2194095
10. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. H Grosjean W Fiers, Gene 1982 18 3 199 209 10.1016/0378- 1119(82)90157-3 6751939
11. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. W Konigsberg GN Godson, Proc Natl Acad Sci U S A 1983 80 3 687 691 6338495 10.1073/pnas.80.3.687
12. Rare codons in E. coli and S. typhimurium signal sequences. DM Burns IR Beacham, FEBS Lett 1985 189 2 318 324 10.1016/0014-5793(85)81048-6 3899723
13. Delineation of coding areas in DNA sequences through assignment of codon probabilities. PW Hinds RD Blake, J Biomol Struct Dyn 1985 3 3 543 549 3917036
14. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. PM Sharp WH Li, Nucleic Acids Res 1986 14 19 7737 7749 3534792 10.1093/nar/14.19.7737
15. The selection-mutation-drift theory of synonymous codon usage. M Bulmer, Genetics 1991 129 3 897 907 1752426
16. DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence. V Bauer DuMont JC Fay PP Calabrese CF Aquadro, Genetics 2004 167 1 171 185 15166145 10.1534/genetics.167.1.171
17. Research Article: Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila. R Nielsen VL Bauer Dumont MJ Hubisz CF Aquadro, Mol Biol Evol 2006
18. Codon bias as a factor in regulating expression via translation rate in the human genome. Y Lavner D Kotlar, Gene 2005 345 1 127 138 10.1016/j.gene.2004.11.035 15716084
19. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. H Akashi, Genetics 1995 139 2 1067 1076 7713409
20. Evolution of protein molecules. TH Jukes Cantor, C. R., Mammalian Protein Metabolism New York, Academic Press, Munro HN, 1969 21 123
21. Statistical significance for genomewide studies. JD Storey R Tibshirani, Proc Natl Acad Sci U S A 2003 100 16 9440 9445 12883005 10.1073/pnas.1530509100
22. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. VL MacKay X Li MR Flory E Turcott GL Law KA Serikawa XL Xu H Lee DR Goodlett R Aebersold LP Zhao DR Morris, Mol Cell Proteomics 2004 3 5 478 489 10.1074/mcp.M300129-MCP200 14766929
23. Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region. C Vilela JE McCarthy, Mol Microbiol 2003 49 4 859 867 10.1046/j.1365-2958.2003.03622.x 12890013
24. Physical evidence for distinct mechanisms of translational control by upstream open reading frames. A Gaba Z Wang T Krishnamoorthy AG Hinnebusch MS Sachs, Embo J 2001 20 22 6453 6463 11707416 10.1093/emboj/20.22.6453
25. Translational regulation of GCN4 and the general amino acid control of yeast. AG Hinnebusch, Annu Rev Microbiol 2005 59 407 450 10.1146/annurev.micro. 59.031805.133833 16153175
26. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. JV Chamary LD Hurst, Genome Biol 2005 6 9 R75 16168082 10.1186/gb-2005-6-9-r75
27. A periodic pattern of mRNA secondary structure created by the genetic code. SA Shabalina AY Ogurtsov NA Spiridonov, Nucleic Acids Res 2006 34 8 2428 2437 16682450 10.1093/nar/gkl287
28. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. JL Parmley JV Chamary LD Hurst, Mol Biol Evol 2006 23 2 301 309 10.1093/molbev/msj035 16221894
29. Exonic Splicing Regulatory Elements Skew Synonymous Codon Usage Near Intron-Exon Boundaries in Mammals. JL Parmley LD Hurst, Mol Biol Evol 2007 17525472
30. Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. LD Hurst, J Mol Evol 2006 63 2 174 182 10.1007/s00239-005-0273-2 16786435
31. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. H Dong L Nilsson CG Kurland, J Mol Biol 1996 260 5 649 663 10.1006/jmbi.1996.0428 8709146
32. The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders. GL Law KS Bickel VL MacKay DR Morris, Genome Biol 2005 6 13 R111 16420678 10.1186/gb-2005-6-13-r111
33. Ribosome-mediated translational pause and protein domain organization. TA Thanaraj P Argos, Protein Sci 1996 5 8 1594 1612 8844849
34. Noise in eukaryotic gene expression. WJ Blake KAE M CR Cantor JJ Collins, Nature 2003 422 6932 633 637 10.1038/nature01546 12687005
35. Noise minimization in eukaryotic gene expression. HB Fraser AE Hirsh G Giaever J Kumm MB Eisen, PLoS Biol 2004 2 6 e137 15124029 10.1371/journal.pbio. 0020137
36. Stochastic mechanisms in gene expression. HH McAdams A Arkin, Proc Natl Acad Sci U S A 1997 94 3 814 819 9023339 10.1073/pnas.94.3.814
37. The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. AM Kierzek J Zaim P Zielenkiewicz, J Biol Chem 2001 276 11 8165 8172 10.1074/jbc.M006264200 11062240
38. Regulation of noise in the expression of a single gene. EM Ozbudak M Thattai I Kurtser AD Grossman A van Oudenaarden, Nat Genet 2002 31 1 69 73 10.1038/ng869 11967532
39. Intrinsic noise in gene regulatory networks. M Thattai A van Oudenaarden, Proc Natl Acad Sci U S A 2001 98 15 8614 8619 11438714 10.1073/pnas.151588598
40. Resources for fungal comparative genomics. http://fungal.genome.duke.edu/
41. TIGR database: Cryptococcus neoformans Genome Project. http://www.tigr.org/tdb/e2k1/cna1/
42. Flybase. http://www.flybase.org
43. UCSC genome bioinformatics. http://genome.ucsc.edu/
44. Saccharomyces genome databse.
45. Broad Institute website. http://www.broad.mit.edu
46. Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. Z Zhang FS Dietrich, Curr Genet 2005 48 2 77 87 10.1007/s00294-005- 0001-x 16012843
47. A high-resolution map of transcription in the yeast genome. L David W Huber M Granovskaia J Toedling CJ Palm L Bofkin T Jones RW Davis LM Steinmetz, Proc Natl Acad Sci U S A 2006 103 14 5320 5325 16569694 10.1073/pnas.0601091103
48. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 7984417 10.1093/nar/22.22.4673
49. Accounting for background nucleotide composition when measuring codon usage bias. JA Novembre, Mol Biol Evol 2002 19 8 1390 1394 12140252
50. PM Sharp AT Lloyd, An Atlas of Drosophila Genes: Sequences and Molecular Features New York, Oxford University Press, Maroni G, 1993 378 397
51. Patterns of nucleotide substitution in Drosophila and mammalian genomes. DA Petrov DL Hartl, Proc Natl Acad Sci U S A 1999 96 4 1475 1479 9990048 10.1073/pnas.96.4.1475
52. PAML: a program package for phylogenetic analysis by maximum likelihood. Z Yang, Comput Appl Biosci 1997 13 5 555 556 9367129
53. Q-Value.
54. The Gene Ontology GO Slim and Subset Guide. http://www.geneontology.org/ GO.slims.shtml