Directed evolution study unveiling key sequence factors that affect translation efficiency in Escherichia coli

Journal of Bioscience and Bioengineering

Volumn 116, Issue 5, 2013, Pages 540-545

  Tsukuda, Miyuki ^a,b   Miyazaki, Kentaro ^a,b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Codon usage; Directed evolution; Green fluorescence protein; MRNA folding; Synonymous mutations; Translation efficiency

Indexed keywords

CODON USAGE; DIRECTED EVOLUTION; GREEN FLUORESCENCE PROTEINS; MRNA FOLDING; SYNONYMOUS MUTATIONS;

BIOSYNTHESIS; EFFICIENCY; ESCHERICHIA COLI; FLUORESCENCE; GENES; MUTAGENESIS; NUCLEIC ACIDS;

COLLECTOR EFFICIENCY;

ARGININE; BACTERIAL DNA; GLYCINE; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; NUCLEOTIDE;

5' UNTRANSLATED REGION; ARTICLE; BACILLUS SUBTILIS; BACTERIAL MUTATION; CODON; ESCHERICHIA COLI; FLUORESCENCE ANALYSIS; GENE EXPRESSION; GENE LIBRARY; GENE SYNTHESIS; GENETIC TRANSCRIPTION AND TRANSLATION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MUTAGENESIS; NONHUMAN; PREDICTION; PROTEIN SECONDARY STRUCTURE; RNA STABILITY;

BACILLUS SUBTILIS; ESCHERICHIA COLI;

CODON USAGE; DIRECTED EVOLUTION; GREEN FLUORESCENCE PROTEIN; MRNA FOLDING; SYNONYMOUS MUTATIONS; TRANSLATION EFFICIENCY;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; CODON; DIRECTED MOLECULAR EVOLUTION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GREEN FLUORESCENT PROTEINS; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN BIOSYNTHESIS; RNA FOLDING; RNA, MESSENGER;

EID: 84885382773     PISSN: 13891723     EISSN: 13474421     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2013.05.013     Document Type: Article

References (29)

1. Studier F.W. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J.Mol. Biol. 1991, 219:37-44.
2. Grodberg J., Dunn J.J. ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. J.Bacteriol. 1988, 170:1245-1253.
3. Schein C.H., Noteborn M.H.M. Production of soluble recombinant protein in bacteria. Biotechnology 1989, 7:1141-1148.
4. Gustafsson C., Govindarajan S., Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol. 2004, 22:346-353.
5. Tuller T., Waldman Y.Y., Kupiec M., Ruppin E. Translation efficiency is determined by both codon bias and folding energy. Proc. Natl. Acad. Sci. USA 2010, 107:3645-3650.
6. 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. 1987, 15:1281-1295.
7. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 1985, 2:13-34.
8. 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. 1981, 151:389-409.
9. Akashi H. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 1994, 136:927-935.
10. Wada K., Wada Y., Ishibashi F., Gojobori T., Ikemura T. Codon usage tabulated from the GeneBank genetic sequence data. Nucleic Acids Res. 1992, 20:2111-2118.
11. Arg4. Mol. Microbiol. 2003, 49:1043-1049.
12. Kim S., Lee S.B. Rare codon clusters at 5'-end influence heterologous expression of archaeal gene in Escherichia coli. Protein Expr. Purif. 2006, 50:49-57.
13. Welch M., Govindarajan S., Ness J.E., Villalobos A., Gurney A., Minshull J., Gustafsson C. Design parameters to control synthetic gene expression in Escherichia coli. PLoS One 2009, 4:e7002.
14. Hall M.N., Gabay J., Débarbouillé M., Schwartz M. Arole for mRNA secondary structure in the control of translation initiation. Nature 1982, 295:616-618.
15. Kudla G., Murray A.W., Tollervey D., Plotkin J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324:255-258.
16. Seo S.W., Yang J., Jung G.Y. Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli. Biotechnol. Bioeng. 2009, 104:611-616.
17. Keller T.E., Mis S.D., Jia K.E., Wilke C.O. Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol. Evol. 2012, 4:80-88.
18. Shine J., Dalgarno L. Determinant of cistron specificity in bacterial ribosomes. Nature 1975, 254:34-38.
19. Stenström C.M., Holmgren E., Isaksson L.A. Cooperative effects by the initiation codon and its flanking regions on translation initiation. Gene 2001, 273:259-265.
20. Milon P., Konevega A.L., Gualerzi C.O., Rodnina M.V. Kinetic checkpoint at a late step in translation initiation. Mol. Cell 2008, 30:712-720.
21. Gu W., Zhou T., Wilke C.O. Auniversal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput. Biol. 2010, 6:e1000664.
22. Miyazaki K., Takenouchi M. Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. Biotechniques 2002, 33:1033-1038.
23. Zhao H., Giver L., Shao Z., Affholter J.A., Arnold F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 1998, 16:258-261.
24. Miyazaki K., Arnold F.H. Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J.Mol. Evol. 1999, 49:716-720.
25. Weiner M.P., Costa G.L., Schoettlin W., Cline J., Mathur E., Bauer J.C. Site-directed mutagenesis of double-stranded DNA by the polymerase chain reaction. Gene 1994, 151:119-123.
26. Sato K., Hamada M., Asai K., Mituyama T. CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 2009, 37:W277-W280.
27. Pédelacq J.D., Cabantous S., Tran T., Terwilliger T.C., Waldo G.S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 2006, 24:79-88.
28. Zhao H., Arnold F.H. Functional and nonfunctional mutations distinguished by random recombination of homologous genes. Proc. Natl. Acad. Sci. USA 1997, 94:7997-8000.
29. Kane J.F. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr. Opin. Biotechnol. 1995, 6:494-500.