Mammalian Mutation Pressure, Synonymous Codon Choice, and mRNA Degradation

Journal of Molecular Evolution

Volumn 57, Issue 6, 2003, Pages 694-701

  Duan, Jubao ^a   Antezana, Marcos A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

CG; Cleavage; Codon usage; Codon usage bias; Context dependent mutation; Dinucleotide; Endoribonuclease; Human; Mammalian; mRNA; Mutation; Noncoding region; Secondary structure; Synonymous codon; TA; Target sequence; Transcribed region; Transcriptome; tRNA pools; UA

Indexed keywords

DNA; MESSENGER RNA; TRANSFER RNA;

AMINO ACID ANALYSIS; ANTICODON; ARTICLE; CODON; CODON USAGE; CORRELATION ANALYSIS; DIAGNOSTIC ACCURACY; DNA TRANSCRIPTION; DROSOPHILA; GENE EXPRESSION REGULATION; GENE MUTATION; IN VITRO STUDY; IN VIVO STUDY; INTRON; MAMMAL; MUTATION; MUTATION PRESSURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRESSURE MEASUREMENT; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA DEGRADATION; SACCHAROMYCES; SYNONYMOUS CODON;

ANIMALS; CHO CELLS; CODON; CRICETINAE; CRICETULUS; DACTINOMYCIN; GC RICH SEQUENCE; HALF-LIFE; HUMANS; MUTATION; RECEPTORS, DOPAMINE D2; RNA, MESSENGER; TIME FACTORS;

MAMMALIA; SACCHAROMYCES;

EID: 0346104825     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2519-1     Document Type: Article

References (44)

1. 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(1):36-43
2. Antezana MA, Kreitman M. Unpublished data
3. Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257:3026-3031
4. Berg OG, Silva PJ (1997) Codon bias in Escherichia coli: The influence of codon context on mutation and selection. Nucleic Acids Res 25(7):1397-1404
5. Beutler E, Gelbart T, Han JH, Koziol JA, Beutler B (1989) Evolution of the genome and the genetic code: Selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc Natl Acad Sci USA 86(1):192-196
6. Candelas G, Candelas T, Ortiz A, Rodriguez O (1983) Translational pauses during a spider fibroin synthesis. Biochem Biophys Res Commun 116(3):1033-1038
7. Caponigro G, Parker R (1996) Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae. Microbiol Rev 60(1):233-249
8. Chavancy G, Garel JP (1981) Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model. Biochimie 63(3):187-195
9. Deana A, Ehrlich R, Reiss C (1996) Synonymous codon selection controls in vivo turnover and amount of mRNA in Escherichia coli bla and ompA genes. J Bacteriol 178(9):2718-2720
10. Duret L, Galtier N (2000) The covariation between TpA deficiency. CpG deficiency, and G + C content of human isochores is due to a mathematical artifact. Mol Biol Evol 17(11):1620-1625
11. Eichler DC, Eales SJ (1983) The effect of RNA secondary structure on the action of a nucleolar endoribonuclease. J Biol Chem 258(16):10049-10053
12. Eichler DC, Tatar TF (1980) Properties of a purified nucleolar ribonuclease from Ehrlich ascites carcinoma cells. Biochemistry 19(13):3016-3022
13. Fiers W, Contreras R, Haegeman G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J. Volckaert G, Ysebaert M (1978) Complete nucleotide-sequence of SV40 DNA. Nature 273:113-120
14. Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9(1):R43-R74
15. Grosjean H, Freirs W (1982) Preferential codon usage in prokaryotic genes: The optimal codon-anti-codon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18:199-209
16. Hoekema A, Kastelein RA, Vasser M, de Boer HA (1987) Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: Experimental approach to study the role of biased codon usage in gene expression. Mol Cell Biol 7(8):2914-2924
17. Josse J, Kaiser AD, Kornberg A (1961) Enzymatic synthesis of deoxyribonucleic acid. 8. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J Biol Chem 236(3):864-875
18. Kafatos FC, Efstratiadis A, Forget BG, Weissman SM (1977) Molecular evolution of human and rabbit beta-globin mRNAs. Molecular evolution of human and rabbit beta-globin messenger-RNAs. Proc Natl Acad Sci USA 74(12):5618-5622
19. Karlin S, Burge C (1995) Dinucleotide relative abundance extremes: A genomic signature. Trends Genet 11(7):283-290
20. Konu O, Li MD (2002) Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. J Mol Evol 54(1):35-41
21. Lenim I, Ross J (2002) Regulation of c-myc mRNA decay by translational pausing in a coding region instability determinant. Mol Cell Biol 22(12):3959-3969
22. Lennon GG, Fraser NW (1983) CpG frequency in large DNA segments. J Mol Evol 19(3-4):286-288
23. Lustig F, Boren T, Claesson C, Simonsson C, Barcisszewska M, Lagerkvist U (1993) The nucleotide in position 33 of the tRNA anticodon loop determines ability of anticodon UCC to discriminate among glycine codons. Proc Natl Acad Sci USA 90:3343-3347
24. Nussinov R (1981a) Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage. J Mol Biol 149(1):125-131
25. Nussinov R (1981b) Nearest neighbor nucleotide patterns. Structural and biological implications. J Biol Chem 256(16):8458-8462
26. Oprea M, Cowell LG, Kepler TB (2001) The targeting of somatic hypermutation closely resembles that of meiotic mutation. J Immunol 166(2):892-899
27. Parker J (1989) Errors and alternatives in reading the universal genetic code. Microbiol Rev 53(3):273-298
28. Parker R, Jacobson A (1990) Translation and a 42-nucleotide segment within the coding region of the mRNA encoded by the MAT alpha 1 gene are involved in promoting rapid mRNA decay in yeast. Proc Natl Acad Sci USA 87(7):2780-2784
29. Perlak FJ, Fuchs RL, Dean DA, McPherson SL, Fischhoff DA (1991) Modification of the coding sequence enhances plant expression of insect control protein genes. Proc Natl Acad Sci USA 88(8):3324-3328
30. Post LE, Nomura M (1979) Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli. Biol Chem 254(21):10604-10606
31. Post LE, Strycharz GD, Nomura M, Lewis H, Dennis PP (1979) Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. Proc Natl Acad Sci USA 76(4):1697-1701
32. Precup J, Parker J (1987) Missense misreading of asparagine codons as a function of codon identity and context. Biol Chem 262(23):11351-11355
33. Qiu L, Moreira A, Kaplan G, Levitz R, Wang JY, Xu C, Drlica K (1998) Degradation of hammerhead ribozymes by human ribonucleases. Mol Gen Genet 258(4):352-362
34. Russell GJ, Subak-Sharpe JH (1967) Similarity of the general designs of protochordates and invertebrates. Nature 266:533-536
35. Salser W (1978) Globin mRNA sequences: Analysis of base pairing and evolutionary implications. Cold Spring Harbor Symp Quant Biol 42(2):985-1002
36. Seffens W, Digby D (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27(7):1578-1584
37. Setlow P (1976) In: Fasman GD (ed) Handbook of biochemistry and molecular biology. CRC Press, Cleveland, OH, pp 312-318
38. Smith DS, Creadon G, Jena PK, Portanova JP, kotzin BL, Wysocki LJ (1996) Di-and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cells. J Immunol 156(7):2642-2652
39. Urrutia AO, Hurst LD (2001) Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 59(3):1191-1199
40. Williamson JR (1994) G-quartet structures in telometic DNA. Annu Rev Biophys Biomol Struct 23:703-730
41. Workman C, Krogh A (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res. 27:4816-4822
42. Zama M (1997) Translational pauses during the synthesis of proteins and mRNA structure. Nucleic Acids Symp Ser 37:179-180
43. Zhou J, Liu WJ, Peng SW, Sun XY, Frazer I (1999) Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. J Virol 73:4972-4982
44. Zolotukhin S, Potter M, Hauswirth WW, Guy J, Muzyczka N (1996) A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells. J Virol 70:4646-4654