Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias

Journal of Molecular Evolution

Volumn 61, Issue 3, 2005, Pages 306-314

  Stenøien, Hans K ^a,c   Stephan, Wolfgang ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF MUNICH   (Germany)

^c NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

mRNA secondary structure; Mutation; Regulation; Selection; Translation

Indexed keywords

MESSENGER RNA;

ARTICLE; BASE PAIRING; CODON; CODON USAGE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE STRUCTURE; HYPOTHESIS; NONHUMAN; RNA STABILITY; THERMODYNAMICS;

ANIMALS; BIAS (EPIDEMIOLOGY); CODON; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; RNA STABILITY; THERMODYNAMICS;

DROSOPHILA MELANOGASTER;

EID: 25144453302     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0271-9     Document Type: Article

References (73)

1. Akashi H (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136:927-935
2. Akashi H (1997) Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene 205:269-278
3. Akashi H (2001) Gene expression and molecular evolution. Curr Opin Genet Dev 11:660-666
4. Akashi H (2003) Translational selection and yeast proteome evolution. Genetics 164:1291-1303
5. Akashi H, Eyre-Walker A (1998) Translational selection and molecular evolution. Curr Opin Genet Dev 8:688-693
6. Akashi H, Gojobori T (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA 99:3696-3700
7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
8. Andersson SGE, Kurland CG (1990) Codon preferences in free-living microorganisms. Microbiol Rev 54:198-210
9. Antezana MA, Kreitman M (1999) The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences. J Mol Evol 49:36-43
10. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953-958
11. Boguski MS, Lowe TM, Tolstoshev CM (1993) dbEST: database for "expressed sequence tags." Nat Genet 4:332-333
12. Bose S, Dutko JA, Zitomer RS (2005) Genetic factors that regulate the attenuation of the general stress response of yeast. Genetics 169:1215-1226
13. Brown TA (1999) Genomes. John Wiley & Sons, New York
14. Bulmer M (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907
15. Carlini DB, Chen Y, Stephan W (2001) The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr. Genetics 159:623-633
16. Chiapello H, Fisacek F, Caboche M, Henaut A (1998) Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209:GC1-GC38
17. Coghlan A, Wolfe KH (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16:1131-1145
18. Comeron JM (2004) Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and introns presence. Genetics 167:1293-1304
19. Comeron JM, Kreitman M (2002) Population, evolutionary and genomic consequences of interference selection. Genetics 161:389-410
20. Comeron JM, Kreitman M, Aguadé M (1999) Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151:239-249
21. Craig EA (1986) The heat shock response. CRC Crit Rev Biochem 18:239-280
22. Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5:105
23. Duan J, Antezana MA (2003) Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J Mol Evol 57:694-701
24. Duret L (2000) tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet 16:287-289
25. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA 96:4482-4487
26. Fennoy SL, Bailey-Serres J (1993) Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons. Nucleic Acids Res 21:5294-5300
27. Francino HP, Ochman H (1999) Isochores result from mutation not selection. Nature 400:30-31
28. Gentles AJ, Karlin S (2001) Genome-scale compositional comparisons in eukaryotes. Genome Res 11:540-546
29. Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10:7055-7074
30. Gouy M, Gautier C, Attimonelli M, Lanave C, di Paola G (1985) ACNUC: portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Comput Appl Biosci 1:167-172
31. Grunberg-Manago M (1999) Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu Rev Genet 33:193-227
32. Guhaniyogi J, Brewer G (2001) Regulation of mRNA stability in mammalian cells. Gene 265:11-23
33. Hey J, Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160:595-608
34. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125:167-188
35. Iida K, Akashi H (2000) A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261:93-105
36. Ikemura T (1981a) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146:1-21
37. Ikemura T (1981b) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli system. J Mol Biol 151:389-409
38. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13-34
39. Jenkins GM, Holmes EC (2003) The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res 92:1-7
40. Kanaya S, Yamada Y, Kudo Y, Ikemura T (1999) 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 238:143-155
41. Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T (2001) 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 53:290-298
42. Karlin S, Campbell AM, Mrazek J (1998) Comparative DNA analysis across diverse genomes. Annu Rev Genet 32:185-225
43. Katz L, Burge CB (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res 13:2042-2051
44. Kliman RM, Hey J (1993) Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol Biol Evol 10:1239-1258
45. Kliman RM, Hey J (1994) The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137:1049-1056
46. Konings DA, Gutell RR (1995) A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1:559-574
47. Li WH (1987) Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J Mol Evol 24:337-345
48. Marais G, Duret L (2001) Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J Mol Evol 52:275-280
49. Margulies EH, Kardia SL, Innis JW (2001) Identification and prevention of a GC content bias in SAGE libraries. Nucleic Acids Res 29:E60
50. Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911-940
51. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343-349
52. Miyasaka H (2002) Translation initiation AUG context varies with codon usage bias and gene length in Drosophila melanogaster. J Mol Evol 55:52-64
53. Morita MT, Kanemori M, Yanagi H, Yura T (2000) Dynamic interplay between antagonistic pathways controlling for the σ32 level in Escherichia coli. Proc Natl Acad Sci USA 97:5860-5865
54. Moriyama EN, Powell JR (1997) Codon usage bias and tRNA abundance in Drosophila. J Mol Evol 45:514-523
55. Mount DW (2001) Bioinformatics: sequence and genome analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
56. Munoz ET, Bogarad LD, Deem MW (2004) Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans. BMC Genomics 5:30
57. Musto H, Cruveiller S, D'Onofrio G, Romero H, Bernardi G (2001) Translational selection on codon usage in Xenopus laevis. Mol Biol Evol 18:1703-1707
58. Norusis MJ (2000) SPSS 10.0 guide to data analysis. Prentice Hall, Upper Saddle River, NJ
59. Pervouchine DD, Graber JH, Kasif S (2003) On the normalization of RNA equilibrium free energy to the length of the sequence. Nucleic Acids Res 31:e49
60. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277
61. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175
62. Sharp PM, Lloyd AT (1993) Codon usage. In: Maroni GP (ed) Atlas of Drosophila genes. Oxford University Press, New York, pp 378-397
63. Sharp PM, Matassi G (1994) Codon usage and genome evolution. Curr Opin Genet Dev 4:851-860
64. Sharp PM, Stenico M, Peden JF, Lloyd AT (1993) Codon usage; mutational bias, translational selection, or both? Biochem Soc Trans 21:835-841
65. Sharp PM, Averof M, Lloyd AT, Matassi G, Peden JF (1995) DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B 349:241-247
66. Shields DC, Sharp PM, Higgins DG, Wright F (1988) "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 5:704-716
67. Stenico M, Lloyd AT, Sharp PM (1994) Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational bias. Nucleic Acids Res 22:2437-2446
68. Stenøien HK (2005) Adaptive basis of codon usage in the haploid moss Physcomitrella patens. Heredity 94:87-93
69. Tinoco I, Bustamante C (1999) How RNA folds. J Mol Biol 293:271-281
70. Tuite MF (1996) RNA processing: death by decapitation for mRNA. Nature 382:577-579
71. Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, Mathews DH, Zuker M (1994) Coaxial stacking of helixes enhances binding of oligonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 91:9218-9222
72. Wolfe K, Sharp PM, Li WH (1989) Mutation rates differ among regions of the mammalian genome. Nature 337:283-285
73. Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J, Clark BFC (eds) RNA biochemistry and biotechnology. NATO ASI Series, Kluwer Academic Publishers, pp 11-43