Combinatorial expression vector engineering for tuning of recombinant protein production in Escherichia coli

Nucleic Acids Research

Volumn 35, Issue 5, 2007, Pages

  Bandmann, Nina ^a   Nygren, Per Åke ^a  

^a ALBANOVA UNIVERSITY CENTER   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; FLUORESCENT DYE; RECOMBINANT PROTEIN; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENETICS; BIOTECHNOLOGICAL PRODUCTION; CELLULAR DISTRIBUTION; COMBINATORIAL LIBRARY; CONTROLLED STUDY; CYTOPLASM; DNA SEQUENCE; ESCHERICHIA COLI; EXPRESSION VECTOR; FLOW CYTOMETRY; GENETIC ANALYSIS; GENETIC ENGINEERING; MASS SPECTROMETRY; MOLECULAR CLONING; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN SYNTHESIS; SEQUENCE ANALYSIS; START CODON; TRINUCLEOTIDE REPEAT; WESTERN BLOTTING; BIOSYNTHESIS; CODON; EVALUATION; GENE EXPRESSION; GENE LIBRARY; GENE VECTOR; GENETICS; METHODOLOGY; PROTEIN ENGINEERING; REPORTER GENE; RNA TRANSLATION;

ESCHERICHIA COLI;

CLONING, MOLECULAR; CODON; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENT DYES; GENE EXPRESSION; GENE LIBRARY; GENES, REPORTER; GENETIC VECTORS; GREEN FLUORESCENT PROTEINS; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PROTEIN ENGINEERING; RECOMBINANT FUSION PROTEINS;

EID: 34247162596     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1171     Document Type: Article

References (45)

1. Jana,S. and Deb,J.K. (2005) Strategies for efficient production of heterologous proteins in Escherichia coli. Appl. Microbiol. Biotechnol., 67, 289-298.
2. Jonasson,P., Liljeqvist,S., Nygren,P.A. and Stahl,S. (2002) Genetic design for facilitated production and recovery of recombinant proteins in Escherichia coli. Biotechnol. Appl. Biochem., 35, 91-105.
3. Baneyx,F. and Mujacic,M. (2004) Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol., 22, 1399-1408.
4. Sorensen,H.P. and Mortensen,K.K. (2005) Advanced genetic strategies for recombinant protein expression in Escherichia coli. J. Biotechnol., 115, 113-128.
5. Shine,J. and Dalgarno,L. (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA, 71, 1342-1346.
6. Hartz,D., McPheeters,D.S. and Gold,L. (1991) Influence of mRNA determinants on translation initiation in Escherichia coli. J. Mol. Biol., 218, 83-97.
7. Chang,J.T., Green,C.B. and Wolf,R.E., Jr. (1995) Inhibition of translation initiation on Escherichia coli gnd mRNA by formation of a long-range secondary structure involving the ribosome binding site and the internal complementary sequence. J. Bacteriol., 177, 6560-6567.
8. de Smit,M.H. and van Duin,J. (1994) Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction. J. Mol. Biol., 235, 173-184.
9. Griswold,K.E., Mahmood,N.A., Iverson,B.L. and Georgiou,G. (2003) 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, 134-142.
10. Pfleger,B.F., Fawzi,N.J. and Keasling,J.D. (2005) Optimization of DsRed production in Escherichia coli: Effect of ribosome binding site sequestration on translation efficiency. Biotechnol. Bioeng., 92, 553-558.
11. Schauder,B. and McCarthy,J.E. (1989) The role of bases upstream of the Shine-Dalgarno region and in the coding sequence in the control of gene expression in Escherichia coli: Translation and stability of mRNAs in vivo. Gene., 78, 59-72.
12. Wang,G., Liu,N. and Yang,K. (1995) High-level expression of prochymosin in Escherichia coli: Effect of the secondary structure of the ribosome binding site. [ Protein Expr. Purif., 6, 284-290.
13. Ringquist,S., Shinedling,S., Barrick,D., Green,L., Binkley,J., Stormo,G.D. and Gold,L. (1992) Translation initiation in Escherichia coli: Sequences within the ribosome-binding site. Mol. Microbiol. 6, 1219-1229.
14. Hrzenjak,A., Artl,A., Knipping,G., Kostner,G., Sattler,W. and Malle,E. (2001) Silent mutations in secondary Shine-Dalgarno sequences in the cDNA of human serum amyloid A4 promotes expression of recombinant protein in Escherichia coli. Protein Eng., 14, 949-952.
15. Kane,J.F. (1995) Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr. Opin. Biotechnol., 6, 494-500.
16. Deana,A., Ehrlich,R. and Reiss,C. (1998) Silent mutations in the Escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo. Nucleic Acids Res., 26 4778-4782.
17. Gonzalez de Valdivia,E.I. and Isaksson,L.A. (2004) A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli. Nucleic Acids Res. 32, 5198-5205.
18. Looman,A.C., Bodlaender,J., Comstock,L.J., Eaton,D., Jhurani,P., de Boer,H.A. and van Knippenberg,P.H. (1987) Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli. EMBO J., 6, 2489-2492.
19. Stenstrom,C.M., Holmgren,E. and Isaksson,L.A. (2001) Cooperative effects by the initiation codon and its flanking regions on translation initiation. Gene., 273, 259-265.
20. Stenstrom,C.M. and Isaksson,L.A. (2002) Influences on translation initiation and early elongation by the messenger RNA region flanking the initiation codon at the 3′ side. Gene, 288, 1-8.
21. Stenstrom,C.M., Jin,H., Major,L.L., Tate,W.P. and Isaksson,L.A. (2001) Codon bias at the 3′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli. Gene, 263, 273-284.
22. Gustafsson,C., Govindarajan,S. and Minshull,J. (2004) Codon bias and heterologous protein expression. Trends Biotechnol., 22, 346-353.
23. Rosenberg,A.H., Goldman,E., Dunn,J.J., Studier,F.W. and Zubay,G. (1993) Effects of consecutive AGG codons on translation in Escherichia coli, demonstrated with a versatile codon test system. J. Bacteriol., 175, 716-722.
24. Cortazzo,P., Cervenansky,C., Marin,M., Reiss,C., Ehrlich,R. and Deana,A. (2002) Silent mutations affect in vivo protein folding in Escherichia coli. Biochem. Biophys. Res. Commun., 293, 537-541.
25. Ruther,U. (1982) pUR 250 allows rapid chemical sequencing of both DNA strands of its inserts. Nucleic Acids Res., 10, 5765-5772.
26. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual 2nd edn. Cold Spring Harbor Laboratory Press, New York.
27. Nilsson,B., Moks,T., Jansson,B., Abrahmsen,L., Elmblad,A., Holmgren,E., Henrichson,C., Jones,T.A. and Uhlen,M. (1987) A synthetic IgG-binding domain based on staphylococcal protein A. Protein Eng. 1, 107-113.
28. Yanofsky,C., Platt,T., Crawford,I.P., Nichols,B.P., Christie,G.E., Horowitz,H., VanCleemput,M. and Wu,A.M. (1981) The complete nucleotide sequence of the tryptophan operon of Escherichia coli. Nucleic Acids Res., 9, 6647-6668.
29. Lee,C.L., Ow,D.S. and Oh,S.K. (2006) Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. J. Microbiol. Methods, 65, 258-267.
30. Winer,J., Jung,C.K., Shackel,I. and Williams,P.M. (1999) Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal. Biochem., 270, 41-49.
31. 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.
32. Sharp,P.M. and Li,W.H. (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res., 14, 7737-7749.
33. Cormack,B.P., Valdivia,R.H. and Falkow,S. (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene, 173, 33-38.
34. Hedhammar,M., Stenvall,M., Lonneborg,R., Nord,O., Sjolin,O., Brismar,H., Uhlen,M., Ottosson,J. and Hober,S. (2005) A novel flow cytometry-based method for analysis of expression levels in Escherichia coli, giving information about precipitated and soluble protein. J. Biotechnol., 119, 133-146.
35. Jonasson,P., Nygren,P.A., Johansson,B.L., Wahren,J., Uhlen,M. and Stahl,S. (1998) Gene fragment polymerization gives increased yields of recombinant human proinsulin C-peptide. Gene, 210, 203-210.
36. Chen,H., Bjerknes,M., Kumar,R. and Jay,E. (1994) Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res., 22, 4953-4957.
37. Kozak,M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.
38. Sorensen,M.A., Kurland,C.G. and Pedersen,S. (1989) Codon usage determines translation rate in Escherichia coli. J. Mol. Biol. 207, 365-377.
39. Sato,T., Terabe,M., Watanabe,H., Gojobori,T., Hori-Takemoto,C. and Miura,K. (2001) 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, 851-860.
40. Wilson,B.S., Kautzer,C.R. and Antelman,D.E. (1994) Increased protein expression through improved ribosome-binding sites obtained by library mutagenesis. Biotechniques, 17, 944-953.
41. Zhelyabovskaya,O.B., Berlin,Y.A. and Birikh,K.R. (2004) Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli. Nucleic Acids Res., 32, e52.
42. Priano,C., Arora,R., Jayant,L. and Mills,D.R. (1997) Translational activation in coliphage Qbeta: On a polycistronic messenger RNA, repression of one gene can activate translation of another. J. Mol. Biol., 271, 299-310.
43. Murakawa,G.J. and Nierlich,D.P. (1989) Mapping the lacZ ribosome binding site by RNA footprinting. Biochemistry, 28, 8067-8072.
44. Arora,P., Oas,T.G. and Myers,J.K. (2004) Fast and faster: A designed variant of the B-domain of protein A folds in 3 microsec. Protein Sci., 13, 847-853.
45. Samuelsson,E., Moks,T., Nilsson,B. and Uhlen,M. (1994) Enhanced in vitro refolding of insulin-like growth factor I using a solubilizing fusion partner. Biochemistry, 33, 4207-4211.