Efficient manipulations of synonymous mutations for controlling translation rate: An analytical approach

Journal of Computational Biology

Volumn 19, Issue 2, 2012, Pages 200-231

  Dana, Alexandra ^a   Tuller, Tamir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

biotechnology; codon bias; gene translation; heterologous gene expression; optimality in biological systems

Indexed keywords

INSULIN; RECOMBINANT PROTEIN;

ALGORITHM; BIOLOGICAL MODEL; BIOSYNTHESIS; CODON; COMPUTER SIMULATION; CONFERENCE PAPER; GENETIC CODE; GENETICS; HUMAN; KINETICS; METABOLISM; MUTATION; NONPARAMETRIC TEST; PROTEIN SYNTHESIS; RIBOSOME; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; CODON; COMPUTER SIMULATION; GENETIC CODE; HUMANS; INSULIN; KINETICS; MODELS, GENETIC; MUTATION; PROTEIN BIOSYNTHESIS; RECOMBINANT PROTEINS; RIBOSOMES; SACCHAROMYCES CEREVISIAE; STATISTICS, NONPARAMETRIC;

EID: 84856740693     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0275     Document Type: Conference Paper

References (37)

1. Abrahmsn, L., Moks, T., Nilsson, B., et al. 1986. Secretion of heterologous gene products to the culture medium of Escherichia coli. Nucleic Acids Res.14, 7487-500.
2. Alberts, B., Johnson, A., Lewis, J., et al. 2002. Molecular biology of the cell. Garland Science.
3. Arava, Y., Wang, Y., Storey, J.D., et al. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100, 3889-3894. (Pubitemid 36418127)
4. Burgess-Brown, N.A., Sharma, S., Sobott, F., et al. 2008. Codon optimization can improve expression of human genes in Escherichia coli: a multi-gene study. Protein Express. Purif. 59, 94-102.
5. Cannarozzi, G., Schraudolph, N.N., Faty, M., et al. 2010. A role for codon order in translation dynamics. Cell 141, 355-367.
6. Comeron, J.M., and Aguad, M. 1998. An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 47, 268-274. (Pubitemid 28455143)
7. Drummond, D.A., and Wilke, C.O. 2009. The evolutionary consequences of erroneous protein synthesis. Nat. Rev. Genet. 10, 715-724.
8. Duret, L., and Mouchiroud, D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. Sci. USA 96, 44824487.
9. Gingold, H., and Pilpel, Y. 2011. Determinants of translation efficiency and accuracy. Mol. Syst. Biol. 7, 481.
10. Gu, W., Zhou, T., and Wilke, C.O. 2010. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput. Biol. 6, e1000664.
11. Gustafsson, C., Govindarajan, S., and Minshull, J. 2004. Codon bias and heterologous protein expression. Trends Biotechnol. 22, 346-353. (Pubitemid 38887543)
12. Heinrich, R., and Rapoport, T.A. 1980. Mathematical modelling of translation of mrna in eucaryotes; steady states, time-dependent processes and application to reticulocytest. J. Theor. Biol. 86, 279-313. (Pubitemid 11255651)
13. Ikemura, T. 1982. Correlation between the abundance of yeast transfer rnas and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol. 158, 573-597. (Pubitemid 12044688)
14. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R.S., et al. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223.
15. Kozak, M. 1987. An analysis of 50-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 15, 8125-8148.
16. Kudla, G., Murray, A.W., Tollervey, D., et al. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science. 324, 255-258.
17. Kurt, F., and Michael, I. 2010. How the sequence of a gene can tune its translation. Cell. 141, 227-229.
18. MacDonald, C.T., Gibbs, J.H., and Pipkin, A.C. 1968. Kinetics of biopolymerization on nucleic acid templates. Biopolymers 6, 1-5.
19. Moks, T., Abrahmsen, L., Holmgren, E., et al. Expression of human insulin-like growth factor i in bacteria: use of optimized gene fusion vectors to facilitate protein purification. Biochemistry 26, 5239-5244.
20. Mueller, S., Coleman, J.R., Papamichail, D., et al. 2010. Live attenuated influenza virus vaccines by computer-aided rational design. Nat. Biotechnol. 28, 723-726.
21. Newman, J.R.S., Ghaemmaghami, S., Ihmels, J., et al. 2006. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846.
22. Plotkin, J.B., and Kudla, G. 2010. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet.12:32-42.
23. Raab, D., Graf, M., Notka, F., et al. 2010. The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. Syst. Synth. Biol. 4, 215-225.
24. Reuveni, S., Meilijson, I., Kupiec, M., et al. 2011. Analysis of translation elongation with a ribosome flow mode. PLoS Comput. Biol. 7, e1002127.
25. Romanos, A.M., Scorer, C.A., and Clare, J.J. 1992. Foreign gene expression in yeast: a review. Yeast 8, 423-488.
26. Sharp, P.M., and Li, W.H. 1987. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281-1295.
27. Shaw, L.B., Zia, R.K.P., and Lee, K.H. 2003. Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys. Rev. E 68, 021910.
28. Taniguchi, Y., Choi, P.J., Li, G. et al. 2010. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329, 533-538.
29. Thomas, C.E., and Ming-Qun, X. 2011. Heterologous gene expression in E. Coli. Humana Press, Totowa, NJ.
30. Tuller, T., Carmi, A., Vestsigian, K., et al. 2010a. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141, 344-354.
31. Tuller, T., Waldman, Y.Y., Kupiec, M., et al. 2010b. Translation efficiency is determined by both codon bias and folding energy. Proc. Natl. Acad. Sci. USA 107, 3645-3650.
32. Tuller, T., Veksler, I., Gazit, N., et al. 2011. Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol. 12, R110.
33. Uemura, S., Aitken, C.E., Korlach, J., et al. 2010. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 464, 1012-1017.
34. Vogel, C., de Sousa Abreu, R., Ko, D., et al. 2010. Sequence signatures and mRNA concentration can explain twothirds of protein abundance variation in a human cell line. Mol. Syst. Biol. 6, 400.
35. Welch, M., Govindarajan, S., Ness, J.E., et al. 2009. Design parameters to control synthetic gene expression in Escherichia coli. PLoS ONE 4, e7002.
36. Wenzel, S.C., and Mü ller, R. 2005. Recent developments towards the heteroluogous expression of complex bacterial natural product biosynthetic pathways. Curr. Opin. Biotechnol. 16, 594-606. (Pubitemid 41654637)
37. Zhang, S., Goldman, E., and Zubay, G. 1994. Clustering of low usage codons and ribosome movement. J. Theor. Biol. 170, 339-354. (Pubitemid 24339399)