Genetic code redundancy and its influence on the encoded polypeptides

Computational and Structural Biotechnology Journal

Volumn 1, Issue 1, 2012, Pages e201204006-

  Spencer, Paige S ^a   Barral, José M ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84865083633     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201204006     Document Type: Short Survey

References (76)

1. Schmeing TM, Ramakrishnan V (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature 461:1234-1242.
2. Steitz TA (2008) A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9:242-253.
3. Bashan A, Yonath A (2008) Correlating ribosome function with highresolution structures. Trends Microbiol 16:326-335.
4. Crick FH (1966) Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 19:548-555.
5. Grosjean H, de Crecy-Lagard V, Marck C (2010) Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett 584:252-264.
6. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905-920.
7. Chan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37:D93-97.
8. Curran JF, Yarus M (1989) Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J Mol Biol 209:65-77.
9. Sorensen MA, Pedersen S (1991) Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J Mol Biol 222:265-280.
10. Varenne S, Buc J, Lloubes R, Lazdunski C (1984) Translation is a nonuniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J Mol Biol 180:549-576.
11. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13-34.
12. Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324:255-258.
13. Sorensen MA, Kurland CG, Pedersen S (1989) Codon usage determines translation rate in Escherichia coli. J Mol Biol 207:365-377.
14. Stadler M, Fire A (2011) Wobble base-pairing slows in vivo translation elongation in metazoans. Rna 17:2063-2073.
15. Takyar S, Hickerson RP, Noller HF (2005) mRNA helicase activity of the ribosome. Cell 120:49-58.
16. Gromadski KB, Rodnina MV (2004) Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell 13:191-200.
17. Fluitt A, Pienaar E, Viljoen H (2007) Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem 31:335-346.
18. Plant EP, Nguyen P, Russ JR, Pittman YR, Nguyen T, et al. (2007) Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae. PLoS One 2:e517.
19. Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, et al. (2010) Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 464:1012-1017.
20. Johansson M, Bouakaz E, Lovmar M, Ehrenberg M (2008) The kinetics of ribosomal peptidyl transfer revisited. Mol Cell 30:589-598.
21. Lee TH, Blanchard SC, Kim HD, Puglisi JD, Chu S (2007) The role of fluctuations in tRNA selection by the ribosome. Proc Natl Acad Sci USA 104:13661-13665.
22. Chu D, Barnes DJ, von der Haar T (2011) The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae. Nucleic Acids Res 39:6705-6714.
23. Ehrenberg M, Kurland CG (1984) Costs of accuracy determined by a maximal growth rate constraint. Q Rev Biophys 17:45-82.
24. Kurland CG, Hughes D, Ehrenberg M (1996) Limitations of translational accuracy. In: Neidhart FC, editor. Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington, D. C: ASM Press, pp. 979-1004.
25. Ikemura T (1981) 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.
26. 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.
27. Percudani R, Pavesi A, Ottonello S (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol 268:322-330.
28. Dong H, Nilsson L, Kurland CG (1996) Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 260:649-663.
29. Heyman T, Agoutin B, Fix C, Dirheimer G, Keith G (1994) Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA (Ser) GCU. FEBS Lett 347:143-146.
30. Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257:3026-3031.
31. Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8:r49-r62.
32. Perriere G, Thioulouse J (2002) Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res 30:4548-4555.
33. Suzuki H, Brown CJ, Forney LJ, Top EM (2008) Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Res 15:357-365.
34. Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292.
35. Sharp PM, Tuohy TM, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125-5143.
36. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223-230.
37. Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871.
38. Hartl FU, Hayer-Hartl M (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295:1852-1858.
39. Kramer G, Boehringer D, Ban N, Bukau B (2009) The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol 16:589-597.
40. Ellis RJ, Minton AP (2006) Protein aggregation in crowded environments. Biol Chem 387:485-497.
41. Hartl FU, Hayer-Hartl M (2009) Converging concepts of protein folding in vitro and in vivo. Nat Struct Mol Biol 16:574-581.
42. Frydman J (2001) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70:603-647.
43. Baneyx F, Mujacic M (2004) Recombinant protein folding and misfolding in Escherichia coli. Nat Biotechnol 22:1399-1408.
44. Dingermann T (2008) Recombinant therapeutic proteins: production platforms and challenges. Biotechnol J 3:90-97.
45. Agashe VR, Guha S, Chang HC, Genevaux P, Hayer-Hartl M, et al. (2004) Function of trigger factor and DnaK in multidomain protein folding: increase in yield at the expense of folding speed. Cell 117:199-209.
46. Kaiser CM, Chang HC, Agashe VR, Lakshmipathy SK, Etchells SA, et al. (2006) Real-time observation of trigger factor function on translating ribosomes. Nature 444:455-460.
47. Gautschi M, Mun A, Ross S, Rospert S (2002) A functional chaperone triad on the yeast ribosome. Proc Natl Acad Sci U S A 99:4209-4214.
48. Spiess C, Meyer AS, Reissmann S, Frydman J (2004) Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets. Trends Cell Biol 14:598-604.
49. Bremer H, Dennis PP (1996) Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhart FC, editor. Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington, D. C: ASM Press, pp. 1553-1569.
50. Mathews MB, Sonenberg N, Hershey JWB (2000) Origins and principles of translational control. In: Sonenberg N, Hershey JWB, Mathews MB, editors. Translational control of gene expression. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp. 1-31.
51. Itano HA (1968) The structure-rate hypothesis and the toll bridge analogy. In: Rich A, Davidson N, editors. Structural Chemistry and Molecular Biology. San Francisco: W. H. Freeman and Company, pp. 275-280.
52. Purvis IJ, Bettany AJ, Santiago TC, Coggins JR, Duncan K, et al. (1987) The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. J Mol Biol 193:413-417.
53. Welch M, Villalobos A, Gustafsson C, Minshull J (2009) You're one in a googol: optimizing genes for protein expression. J R Soc Interface 6 Suppl 4:S467-476.
54. Angov E (2011) Codon usage: nature's roadmap to expression and folding of proteins. Biotechnol J 6:650-659.
55. Siller E, De Zwaan DC, Anderson JF, Freeman BC, Barral JM (2010) Slowing bacterial translation speed enhances eukaryotic protein folding efficiency. J Mol Biol 396:1310-1318.
56. Sharp PM, Li WH (1987) The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-1295.
57. Clarke TF IV, Clark PL (2008) Rare codons cluster. PLoS One 3:e34l2.
58. Krasheninnikov IA, Komar AA, Adzhubei IA (1989) Role of the code redundancy in determining cotranslational protein folding. Biokhimiia 54, 187-200.
59. Crombie T, Boyle JP, Coggins JR, Brown AJ (1994) The folding of the bifunctional TRP3 protein in yeast is influenced by a translational pause which lies in a region of structural divergence with Escherichia coli indoleglycerol-phosphate synthase. Eur J Biochem 226, 657-664.
60. Thanaraj TA, Argos P (1996) Protein secondary structural types are differentially coded on messenger RNA. Protein Sci 5, 1973-1983.
61. Thanaraj TA, Argos P (1996) Ribosome-mediated translational pause and protein domain organization. Protein Sci 5, 1594-1612.
62. Brunak S, Engelbrecht J (1996) Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level. Proteins 25, 237-252.
63. Adzhubei AA, Adzhubei IA, Krasheninnikov IA, Neidle S (1996) Nonrandom usage of 'degenerate' codons is related to protein three-dimensional structure. FEBS Lett 399, 78-82.
64. Ivanov IG, Saraffova AA, Abouhaidar MG (1997) Unusual effect of clusters of rare arginine (AGG) codons on the expression of human interferon alpha 1 gene in Escherichia coli. Int J Biochem Cell Biol 29, 659-666.
65. Komar AA, Guillemet E, Reiss C, Cullin C (1998) Enhanced expression of the yeast Ure2 protein in Escherichia coli: the effect of synonymous codon substitutions at a selected place in the gene. Biol Chem 379, 1295-1300.
66. Komar AA, Lesnik T, Reiss C (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett 462, 387-391.
67. Gupta SK, Majumdar S, Bhattacharya TK, Ghosh TC (2000) Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem Biophys Res Commun 269, 692-696.
68. Maklioul CH, Trifonov EN (2002) Distribution of rare triplets along mRNA and their relation to protein folding. J Biomol Struct Dyn 20, 413-420.
69. Gu W, Zhou T, Ma J, Sun X, Lu Z (2003) Folding type specific secondary structure propensities of synonymous codons. IEEE Trans Nanobiosdence 2, 150-157.
70. Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, et al. (2007) A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525-528.
71. Hamano T, Matsuo K, Hibi Y, Victoriano AF, Takahashi N, et al. (2007) A single-nucleotide synonymous mutation in the gag gene controlling human immunodeficiency virus type 1 virion production. J Virol 81, 1528-1533.
72. Zhang G, Hubalewska M, Ignatova Z (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol 16, 274-280.
73. Zhou T, Weems M, Wilke CO (2009) Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol 26, 1571-1580.
74. Saunders R, Deane CM (2010) Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res 38, 6719-6728.
75. Zhang F, Saha S, Shabahna SA, Kashina A (2010) Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science 329, 1534-1537.
76. Schmeing TM, Voorhees RM, Kelley AC, Ramakrishnan V (2011) How mutations in tRNA distant from the anticodon affect the fidelity of decoding. Nat Struct Mol Biol 18, 432-436.