Codon bias and heterologous protein expression

Trends in Biotechnology

Volumn 22, Issue 7, 2004, Pages 346-353

  Gustafsson, Claes ^a   Govindarajan, Sridhar ^a   Minshull, Jeremy ^a  

^a DNA20 Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; COSTS; PROTEINS; RNA;

PROTEINS EXPRESSION; REGULATORY ELEMENTS;

GENES;

AMINO ACID SEQUENCE; BIOTECHNOLOGY; CODING; CODON; GENE SEQUENCE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW; RNA TRANSLATION;

CLONING, MOLECULAR; CODON; GENE EXPRESSION REGULATION; PROTEIN ENGINEERING; PROTEINS; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 3042782585     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2004.04.006     Document Type: Review

References (76)

1. Itakura K., et al. Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. Science. 198:1977;1056-1063
2. Wu X., et al. Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance. Biochem. Biophys. Res. Commun. 313:2004;89-96
3. Higgins S.J., Hames B.D. Protein Expression: A Practical Approach. 1999;Oxford University Press
4. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:1982;7055-7074
5. Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 18:1982;199-209
6. Knight R.D., et al. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2:2001;. RESEARCH0010
7. Andersson G.E., Kurland C.G. An extreme codon preference strategy: codon reassignment. Mol. Biol. Evol. 8:1991;530-544
8. Kane J.F. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr. Opin. Biotechnol. 6:1995;494-500
9. Sharp P.M., Li W.H. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1987;1281-1295
10. Carbone A., et al. Codon adaptation index as a measure of dominating codon bias. Bioinformatics. 19:2003;2005-2015
11. Lithwick G., Margalit H. Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res. 13:2003;2665-2673
12. Ikemura T. 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 translational system. J. Mol. Biol. 151:1981;389-409
13. Bulmer M. Coevolution of codon usage and transfer RNA abundance. Nature. 325:1987;728-730
14. Massey S.E., et al. Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp. Genome Res. 13:2003;544-557
15. Santos M.A.S., et al. Driving change: the evolution of alternative genetic codes. Trends Genet. 20:2004;95-102
16. Knight R.D., et al. Rewiring the keyboard: evolvability of the genetic code. Nat. Rev. Genet. 2:2001;49-58
17. Björk G.R. Escherichia coli and Salmonella: Cellular and Molecular Biology. Neidhardt F.C., et al. 1996;861-886 ASM Press
18. Urbonavicius J., et al. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J. 20:2001;4863-4873
19. Li J.N., Björk G.R. 1-methylguanosine deficiency of tRNA influences cognate codon interaction and metabolism in Salmonella typhimurium. J. Bacteriol. 177:1995;6593-6600
20. Wahab S.Z., et al. Effects of tRNA(1Leu) overproduction in Escherichia coli. Mol. Microbiol. 7:1993;253-263
21. Gefter M.L., Russell R.L. Role modifications in tyrosine transfer RNA: a modified base affecting ribosome binding. J. Mol. Biol. 39:1969;145-157
22. Wilson R.K., Roe B.A. Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA. Proc. Natl. Acad. Sci. U. S. A. 86:1989;409-413
23. Kurland C., Gallant J. Errors of heterologous protein expression. Curr. Opin. Biotechnol. 7:1996;489-493
24. Kink J.A., et al. Efficient expression of the Paramecium calmodulin gene in Escherichia coli after four TAA-to-CAA changes through a series of polymerase chain reactions. J. Protozool. 38:1991;441-447
25. Nambiar K.P., et al. Total synthesis and cloning of a gene coding for the ribonuclease S protein. Science. 223:1984;1299-1301
26. Feng L., et al. High-level expression and mutagenesis of recombinant human phosphatidylcholine transfer protein using a synthetic gene: evidence for a C-terminal membrane binding domain. Biochemistry. 39:2000;15399-15409
27. Deng T. Bacterial expression and purification of biologically active mouse c-Fos proteins by selective codon optimization. FEBS Lett. 409:1997;269-272
28. Graf M., et al. Concerted action of multiple cis-acting sequences is required for Rev dependence of late human immunodeficiency virus type 1 gene expression. J. Virol. 74:2000;10822-10826
29. Cormack B.P., et al. Yeast-enhanced green fluorescent protein (yEGFP)a reporter of gene expression in Candida albicans. Microbiology. 143:1997;303-311
30. Collins K., Gandhi L. The reverse transcriptase component of the Tetrahymena telomerase ribonucleoprotein complex. Proc. Natl. Acad. Sci. U. S. A. 95:1998;8485-8490
31. Hoekema A., et al. 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. 7:1987;2914-2924
32. Deana A., et al. Silent mutations in the Escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo. Nucleic Acids Res. 26:1998;4778-4782
33. Sato T., et al. Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency. J. Biochem. (Tokyo). 129:2001;851-860
34. Stenstrom C.M., Isaksson L.A. Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3′ side. Gene. 288:2002;1-8
35. Griswold K.E., et al. Effects of codon usage versus putative 5′-mRNA structure on the expression of Fusarium solani cutinase in the Escherichia coli cytoplasm. Protein Expr. Purif. 27:2003;134-142
36. Ishida M., et al. Overexpression in Escherichia coli of the AT-rich trpA and trpB genes from the hyperthermophilic archaeon Pyrococcus furiosus. FEMS Microbiol. Lett. 216:2002;179-183
37. Klasen M., Wabl M. Silent point mutation in DsRed resulting in enhanced relative fluorescence intensity. Biotechniques. 36:2004;236-237
38. Williams D.P., et al. Design, synthesis and expression of a human interleukin-2 gene incorporating the codon usage bias found in highly expressed Escherichia coli genes. Nucleic Acids Res. 16:1988;10453-10467
39. Makoff A.J., et al. Expression of tetanus toxin fragment C in E. coli: high level expression by removing rare codons. Nucleic Acids Res. 17:1989;10191-10202
40. Perlak F.J., et al. Modification of the coding sequence enhances plant expression of insect control protein genes. Proc. Natl. Acad. Sci. U. S. A. 88:1991;3324-3328
41. Kotula L., Curtis P.J. Evaluation of foreign gene codon optimization in yeast: expression of a mouse IG kappa chain. Biotechnology (N. Y.). 9:1991;1386-1389
42. Jensen L.G., et al. Transgenic barley expressing a protein-engineered, thermostable (1, 3-1, 4)-beta-glucanase during germination. Proc. Natl. Acad. Sci. U. S. A. 93:1996;3487-3491
43. Hu X., et al. Specific replacement of consecutive AGG codons results in high-level expression of human cardiac troponin T in Escherichia coli. Protein Expr. Purif. 7:1996;289-293
44. Haas J., et al. Codon usage limitation in the expression of HIV-1 envelope glycoprotein. Curr. Biol. 6:1996;315-324
45. Zolotukhin S., et al. A 'humanized' green fluorescent protein cDNA adapted for high-level expression in mammalian cells. J. Virol. 70:1996;4646-4654
46. Ejdeback M., et al. Effects of codon usage and vector-host combinations on the expression of spinach plastocyanin in Escherichia coli. Protein Expr. Purif. 11:1997;17-25
47. Hale R.S., Thompson G. Codon optimization of the gene encoding a domain from human type 1 neurofibromin protein results in a threefold improvement in expression level in Escherichia coli. Protein Expr. Purif. 12:1998;185-188
48. Uchijima M., et al. Optimization of codon usage of plasmid DNA vaccine is required for the effective MHC class I-restricted T cell responses against an intracellular bacterium. J. Immunol. 161:1998;5594-5599
49. Johansson A.S., et al. Use of silent mutations in cDNA encoding human glutathione transferase M2-2 for optimized expression in Escherichia coli. Protein Expr. Purif. 17:1999;105-112
50. Alexeyev M.F., Winkler H.H. Gene synthesis, bacterial expression and purification of the Rickettsia prowazekii ATP/ADP translocase. Biochim. Biophys. Acta. 1419:1999;299-306
51. Zhou J., et al. Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability. J. Virol. 73:1999;4972-4982
52. Vervoort E.B., et al. Optimizing heterologous expression in dictyostelium: importance of 5′ codon adaptation. Nucleic Acids Res. 28:2000;2069-2074
53. Batard Y., et al. Increasing expression of P450 and P450-reductase proteins from monocots in heterologous systems. Arch. Biochem. Biophys. 379:2000;161-169
54. zur Megede J., et al. Increased expression and immunogenicity of sequence-modified human immunodeficiency virus type 1 gag gene. J. Virol. 74:2000;2628-2635
55. Massaer M., et al. High-level expression in mammalian cells of recombinant house dust mite allergen ProDer p 1 with optimized codon usage. Int. Arch. Allergy Immunol. 125:2001;32-43
56. Narum D.L., et al. Codon optimization of gene fragments encoding Plasmodium falciparum merzoite proteins enhances DNA vaccine protein expression and immunogenicity in mice. Infect. Immun. 69:2001;7250-7253
57. Valencik M.L., McDonald J.A. Codon optimization markedly improves doxycycline regulated gene expression in the mouse heart. Transgenic Res. 10:2001;269-275
58. Leder C., et al. Enhancement of capsid gene expression: preparing the human papillomavirus type 16 major structural gene L1 for DNA vaccination purposes. J. Virol. 75:2001;9201-9209
59. Woo J.H., et al. Gene optimization is necessary to express a bivalent anti-human anti-T cell immunotoxin in Pichia pastoris. Protein Expr. Purif. 25:2002;270-282
60. Shimshek D.R., et al. Codon-improved Cre recombinase (iCre) expression in the mouse. Genesis. 32:2002;19-26
61. Outchkourov N.S., et al. Optimization of the expression of equistatin in Pichia pastoris. Protein Expr. Purif. 24:2002;18-24
62. Li Y., et al. Cloning and hemolysin-mediated secretory expression of a codon-optimized synthetic human interleukin-6 gene in Escherichia coli. Protein Expr. Purif. 25:2002;437-447
63. Sinclair G., Choy F.Y. Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris. Protein Expr. Purif. 26:2002;96-105
64. Hamdan F.F., et al. Codon optimization improves heterologous expression of a Schistosoma mansoni cDNA in HEK293 cells. Parasitol. Res. 88:2002;583-586
65. Slimko E.M., Lester H.A. Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels. J. Neurosci. Methods. 124:2003;75-81
66. Bradel-Tretheway B.G., et al. Effects of codon-optimization on protein expression by the human herpesvirus 6 and 7 U51 open reading frame. J. Virol. Methods. 111:2003;145-156
67. Gao F., et al. Codon usage optimization of HIV type 1 subtype C gag, pol, env, and nef genes: in vitro expression and immune responses in DNA-vaccinated mice. AIDS Res. Hum. Retroviruses. 19:2003;817-823
68. Li A., et al. Optimized gene synthesis and high expression of human interleukin-18. Protein Expr. Purif. 32:2003;110-118
69. Disbrow G.L., et al. Codon optimization of the HPV-16 E5 gene enhances protein expression. Virology. 311:2003;105-114
70. Cid-Arregui A., et al. A synthetic E7 gene of human papillomavirus type 16 that yields enhanced expression of the protein in mammalian cells and is useful for DNA immunization studies. J. Virol. 77:2003;4928-4937
71. Yadava A., Ockenhouse C.F. Effect of codon optimization on expression levels of a functionally folded malaria vaccine candidate in prokaryotic and eukaryotic expression systems. Infect. Immun. 71:2003;4961-4969
72. Henaut A., Danchin A. Analysis and predictions from Escherichia coli sequences. Neidhardt F.C., et al. Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology. Vol. 2:1996;2047-2066 ASM press
73. Boycheva S., et al. Codon pairs in the genome of Escherichia coli. Bioinformatics. 19:2003;987-998
74. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410
75. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:2003;3406-3415
76. Satya R.V., et al. A pattern matching algorithm for codon optimization and CpG motif engineering in DNA expression vectors. Titsworth F. The Second International IEEE Computer Society Computational Systems Bioinformatics Conference. 2003;294-305 The Institute of Electrical and Electronics Engineers